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 java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.Component;
  26 import java.awt.Rectangle;
  27 import java.awt.Toolkit;
  28 import java.awt.datatransfer.Clipboard;
  29 import java.awt.datatransfer.DataFlavor;
  30 import java.awt.datatransfer.StringSelection;
  31 import java.awt.datatransfer.Transferable;
  32 import java.awt.dnd.DnDConstants;
  33 import java.awt.dnd.DropTargetDragEvent;
  34 import java.awt.dnd.DropTargetDropEvent;
  35 import java.awt.dnd.DropTargetEvent;
  36 import java.awt.dnd.DropTargetListener;
  37 import java.awt.event.ActionEvent;
  38 import java.awt.event.ActionListener;
  39 import java.awt.event.FocusAdapter;
  40 import java.awt.event.FocusEvent;
  41 import java.awt.event.ItemEvent;
  42 import java.awt.event.ItemListener;
  43 import java.awt.event.KeyAdapter;
  44 import java.awt.event.KeyEvent;
  45 import java.awt.event.MouseEvent;
  46 import java.awt.print.PageFormat;
  47 import java.awt.print.PrinterJob;
  48 import java.beans.PropertyChangeEvent;
  49 import java.io.File;
  50 import java.io.FileWriter;
  51 import java.io.IOException;
  52 import java.io.PrintWriter;
  53 import java.net.URL;
  54 import java.util.ArrayList;
  55 import java.util.Arrays;
  56 import java.util.Deque;
  57 import java.util.Enumeration;
  58 import java.util.Hashtable;
  59 import java.util.List;
  60 import java.util.Vector;
  61
  62 import javax.swing.ButtonGroup;
  63 import javax.swing.JCheckBoxMenuItem;
  64 import javax.swing.JComponent;
  65 import javax.swing.JEditorPane;
  66 import javax.swing.JInternalFrame;
  67 import javax.swing.JLabel;
  68 import javax.swing.JLayeredPane;
  69 import javax.swing.JMenu;
  70 import javax.swing.JMenuItem;
  71 import javax.swing.JPanel;
  72 import javax.swing.JScrollPane;
  73 import javax.swing.SwingUtilities;
  74
  75 import ext.vamsas.ServiceHandle;
  76 import jalview.analysis.AlignmentSorter;
  77 import jalview.analysis.AlignmentUtils;
  78 import jalview.analysis.CrossRef;
  79 import jalview.analysis.Dna;
  80 import jalview.analysis.GeneticCodeI;
  81 import jalview.analysis.ParseProperties;
  82 import jalview.analysis.SequenceIdMatcher;
  83 import jalview.api.AlignExportSettingsI;
  84 import jalview.api.AlignViewControllerGuiI;
  85 import jalview.api.AlignViewControllerI;
  86 import jalview.api.AlignViewportI;
  87 import jalview.api.AlignmentViewPanel;
  88 import jalview.api.FeatureSettingsControllerI;
  89 import jalview.api.FeatureSettingsModelI;
  90 import jalview.api.SplitContainerI;
  91 import jalview.api.ViewStyleI;
  92 import jalview.api.analysis.SimilarityParamsI;
  93 import jalview.bin.Cache;
  94 import jalview.bin.Jalview;
  95 import jalview.commands.CommandI;
  96 import jalview.commands.EditCommand;
  97 import jalview.commands.EditCommand.Action;
  98 import jalview.commands.OrderCommand;
  99 import jalview.commands.RemoveGapColCommand;
 100 import jalview.commands.RemoveGapsCommand;
 101 import jalview.commands.SlideSequencesCommand;
 102 import jalview.commands.TrimRegionCommand;
 103 import jalview.datamodel.AlignExportSettingsAdapter;
 104 import jalview.datamodel.AlignedCodonFrame;
 105 import jalview.datamodel.Alignment;
 106 import jalview.datamodel.AlignmentAnnotation;
 107 import jalview.datamodel.AlignmentExportData;
 108 import jalview.datamodel.AlignmentI;
 109 import jalview.datamodel.AlignmentOrder;
 110 import jalview.datamodel.AlignmentView;
 111 import jalview.datamodel.ColumnSelection;
 112 import jalview.datamodel.HiddenColumns;
 113 import jalview.datamodel.PDBEntry;
 114 import jalview.datamodel.SeqCigar;
 115 import jalview.datamodel.Sequence;
 116 import jalview.datamodel.SequenceGroup;
 117 import jalview.datamodel.SequenceI;
 118 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 119 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 120 import jalview.io.AlignmentProperties;
 121 import jalview.io.AnnotationFile;
 122 import jalview.io.BackupFiles;
 123 import jalview.io.BioJsHTMLOutput;
 124 import jalview.io.DataSourceType;
 125 import jalview.io.FileFormat;
 126 import jalview.io.FileFormatI;
 127 import jalview.io.FileFormats;
 128 import jalview.io.FileLoader;
 129 import jalview.io.FileParse;
 130 import jalview.io.FormatAdapter;
 131 import jalview.io.HtmlSvgOutput;
 132 import jalview.io.IdentifyFile;
 133 import jalview.io.JPredFile;
 134 import jalview.io.JalviewFileChooser;
 135 import jalview.io.JalviewFileView;
 136 import jalview.io.JnetAnnotationMaker;
 137 import jalview.io.NewickFile;
 138 import jalview.io.ScoreMatrixFile;
 139 import jalview.io.TCoffeeScoreFile;
 140 import jalview.io.vcf.VCFLoader;
 141 import jalview.jbgui.GAlignFrame;
 142 import jalview.project.Jalview2XML;
 143 import jalview.schemes.ColourSchemeI;
 144 import jalview.schemes.ColourSchemes;
 145 import jalview.schemes.ResidueColourScheme;
 146 import jalview.schemes.TCoffeeColourScheme;
 147 import jalview.util.HttpUtils;
 148 import jalview.util.ImageMaker.TYPE;
 149 import jalview.util.MessageManager;
 150 import jalview.util.Platform;
 151 import jalview.viewmodel.AlignmentViewport;
 152 import jalview.viewmodel.ViewportRanges;
 153 import jalview.ws.DBRefFetcher;
 154 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 155 import jalview.ws.jws1.Discoverer;
 156 import jalview.ws.jws2.Jws2Discoverer;
 157 import jalview.ws.jws2.jabaws2.Jws2Instance;
 158 import jalview.ws.seqfetcher.DbSourceProxy;
 159
 160 /**
 161  * DOCUMENT ME!
 162  *
 163  * @author $author$
 164  * @version $Revision$
 165  */
 166 @SuppressWarnings("serial")
 167 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 168         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 169 {
 170
 171   public static final int DEFAULT_WIDTH = 700;
 172
 173   public static final int DEFAULT_HEIGHT = 500;
 174
 175   /*
 176    * The currently displayed panel (selected tabbed view if more than one)
 177    */
 178   public AlignmentPanel alignPanel;
 179
 180   AlignViewport viewport;
 181
 182   public AlignViewControllerI avc;
 183
 184   List<AlignmentPanel> alignPanels = new ArrayList<>();
 185
 186   /**
 187    * Last format used to load or save alignments in this window
 188    */
 189   FileFormatI currentFileFormat = null;
 190
 191   /**
 192    * Current filename for this alignment
 193    */
 194   String fileName = null;
 195
 196   File fileObject;
 197
 198   /**
 199    * Creates a new AlignFrame object with specific width and height.
 200    *
 201    * @param al
 202    * @param width
 203    * @param height
 204    */
 205   public AlignFrame(AlignmentI al, int width, int height)
 206   {
 207     this(al, null, width, height);
 208   }
 209
 210   /**
 211    * Creates a new AlignFrame object with specific width, height and
 212    * sequenceSetId
 213    *
 214    * @param al
 215    * @param width
 216    * @param height
 217    * @param sequenceSetId
 218    */
 219   public AlignFrame(AlignmentI al, int width, int height,
 220           String sequenceSetId)
 221   {
 222     this(al, null, width, height, sequenceSetId);
 223   }
 224
 225   /**
 226    * Creates a new AlignFrame object with specific width, height and
 227    * sequenceSetId
 228    *
 229    * @param al
 230    * @param width
 231    * @param height
 232    * @param sequenceSetId
 233    * @param viewId
 234    */
 235   public AlignFrame(AlignmentI al, int width, int height,
 236           String sequenceSetId, String viewId)
 237   {
 238     this(al, null, width, height, sequenceSetId, viewId);
 239   }
 240
 241   /**
 242    * new alignment window with hidden columns
 243    *
 244    * @param al
 245    *          AlignmentI
 246    * @param hiddenColumns
 247    *          ColumnSelection or null
 248    * @param width
 249    *          Width of alignment frame
 250    * @param height
 251    *          height of frame.
 252    */
 253   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 254           int height)
 255   {
 256     this(al, hiddenColumns, width, height, null);
 257   }
 258
 259   /**
 260    * Create alignment frame for al with hiddenColumns, a specific width and
 261    * height, and specific sequenceId
 262    *
 263    * @param al
 264    * @param hiddenColumns
 265    * @param width
 266    * @param height
 267    * @param sequenceSetId
 268    *          (may be null)
 269    */
 270   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 271           int height, String sequenceSetId)
 272   {
 273     this(al, hiddenColumns, width, height, sequenceSetId, null);
 274   }
 275
 276   /**
 277    * Create alignment frame for al with hiddenColumns, a specific width and
 278    * height, and specific sequenceId
 279    *
 280    * @param al
 281    * @param hiddenColumns
 282    * @param width
 283    * @param height
 284    * @param sequenceSetId
 285    *          (may be null)
 286    * @param viewId
 287    *          (may be null)
 288    */
 289   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 290           int height, String sequenceSetId, String viewId)
 291   {
 292     setSize(width, height);
 293
 294     if (al.getDataset() == null)
 295     {
 296       al.setDataset(null);
 297     }
 298
 299     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 300
 301     alignPanel = new AlignmentPanel(this, viewport);
 302
 303     addAlignmentPanel(alignPanel, true);
 304     init();
 305   }
 306
 307   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 308           HiddenColumns hiddenColumns, int width, int height)
 309   {
 310     setSize(width, height);
 311
 312     if (al.getDataset() == null)
 313     {
 314       al.setDataset(null);
 315     }
 316
 317     viewport = new AlignViewport(al, hiddenColumns);
 318
 319     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 320     {
 321       viewport.hideSequence(hiddenSeqs);
 322     }
 323     alignPanel = new AlignmentPanel(this, viewport);
 324     addAlignmentPanel(alignPanel, true);
 325     init();
 326   }
 327
 328   /**
 329    * Make a new AlignFrame from existing alignmentPanels
 330    *
 331    * @param ap
 332    *          AlignmentPanel
 333    * @param av
 334    *          AlignViewport
 335    */
 336   public AlignFrame(AlignmentPanel ap)
 337   {
 338     viewport = ap.av;
 339     alignPanel = ap;
 340     addAlignmentPanel(ap, false);
 341     init();
 342   }
 343
 344   /**
 345    * initalise the alignframe from the underlying viewport data and the
 346    * configurations
 347    */
 348   void init()
 349   {
 350     // setBackground(Color.white); // BH 2019
 351
 352     if (!Jalview.isHeadlessMode())
 353     {
 354       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 355     }
 356
 357     avc = new jalview.controller.AlignViewController(this, viewport,
 358             alignPanel);
 359     if (viewport.getAlignmentConservationAnnotation() == null)
 360     {
 361       // BLOSUM62Colour.setEnabled(false);
 362       conservationMenuItem.setEnabled(false);
 363       modifyConservation.setEnabled(false);
 364       // PIDColour.setEnabled(false);
 365       // abovePIDThreshold.setEnabled(false);
 366       // modifyPID.setEnabled(false);
 367     }
 368
 369     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 370             "No sort");
 371
 372     if (sortby.equals("Id"))
 373     {
 374       sortIDMenuItem_actionPerformed(null);
 375     }
 376     else if (sortby.equals("Pairwise Identity"))
 377     {
 378       sortPairwiseMenuItem_actionPerformed(null);
 379     }
 380
 381     this.alignPanel.av
 382             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 383
 384     setMenusFromViewport(viewport);
 385     buildSortByAnnotationScoresMenu();
 386     calculateTree.addActionListener(new ActionListener()
 387     {
 388
 389       @Override
 390       public void actionPerformed(ActionEvent e)
 391       {
 392         openTreePcaDialog();
 393       }
 394     });
 395     buildColourMenu();
 396
 397     if (Desktop.desktop != null)
 398     {
 399       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 400       if (!Platform.isJS())
 401       {
 402         addServiceListeners();
 403       }
 404       setGUINucleotide();
 405     }
 406
 407     if (viewport.getWrapAlignment())
 408     {
 409       wrapMenuItem_actionPerformed(null);
 410     }
 411
 412     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 413     {
 414       this.overviewMenuItem_actionPerformed(null);
 415     }
 416
 417     addKeyListener();
 418
 419     final List<AlignmentViewPanel> selviews = new ArrayList<>();
 420     final List<AlignmentPanel> origview = new ArrayList<>();
 421     final String menuLabel = MessageManager
 422             .getString("label.copy_format_from");
 423     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 424             new ViewSetProvider()
 425             {
 426
 427               @Override
 428               public AlignmentPanel[] getAllAlignmentPanels()
 429               {
 430                 origview.clear();
 431                 origview.add(alignPanel);
 432                 // make an array of all alignment panels except for this one
 433                 List<AlignmentPanel> aps = new ArrayList<>(
 434                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 435                 aps.remove(AlignFrame.this.alignPanel);
 436                 return aps.toArray(new AlignmentPanel[aps.size()]);
 437               }
 438             }, selviews, new ItemListener()
 439             {
 440
 441               @Override
 442               public void itemStateChanged(ItemEvent e)
 443               {
 444                 if (origview.size() > 0)
 445                 {
 446                   final AlignmentPanel ap = origview.get(0);
 447
 448                   /*
 449                    * Copy the ViewStyle of the selected panel to 'this one'.
 450                    * Don't change value of 'scaleProteinAsCdna' unless copying
 451                    * from a SplitFrame.
 452                    */
 453                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 454                           .getViewStyle();
 455                   boolean fromSplitFrame = selviews.get(0)
 456                           .getAlignViewport().getCodingComplement() != null;
 457                   if (!fromSplitFrame)
 458                   {
 459                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 460                             .getViewStyle().isScaleProteinAsCdna());
 461                   }
 462                   ap.getAlignViewport().setViewStyle(vs);
 463
 464                   /*
 465                    * Also rescale ViewStyle of SplitFrame complement if there is
 466                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 467                    * the whole ViewStyle (allow cDNA protein to have different
 468                    * fonts)
 469                    */
 470                   AlignViewportI complement = ap.getAlignViewport()
 471                           .getCodingComplement();
 472                   if (complement != null && vs.isScaleProteinAsCdna())
 473                   {
 474                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 475                     ((SplitFrame) af.getSplitViewContainer())
 476                             .adjustLayout();
 477                     af.setMenusForViewport();
 478                   }
 479
 480                   ap.updateLayout();
 481                   ap.setSelected(true);
 482                   ap.alignFrame.setMenusForViewport();
 483
 484                 }
 485               }
 486             });
 487     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 488             .indexOf("devel") > -1
 489             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 490                     .indexOf("test") > -1)
 491     {
 492       formatMenu.add(vsel);
 493     }
 494     addFocusListener(new FocusAdapter()
 495     {
 496       @Override
 497       public void focusGained(FocusEvent e)
 498       {
 499         Jalview.setCurrentAlignFrame(AlignFrame.this);
 500       }
 501     });
 502
 503   }
 504
 505   /**
 506    * Change the filename and format for the alignment, and enable the 'reload'
 507    * button functionality.
 508    *
 509    * @param file
 510    *          valid filename
 511    * @param format
 512    *          format of file
 513    */
 514   public void setFileName(String file, FileFormatI format)
 515   {
 516     fileName = file;
 517     setFileFormat(format);
 518     reload.setEnabled(true);
 519   }
 520
 521   /**
 522    * JavaScript will have this, maybe others. More dependable than a file name
 523    * and maintains a reference to the actual bytes loaded.
 524    *
 525    * @param file
 526    */
 527   public void setFileObject(File file)
 528   {
 529     this.fileObject = file;
 530   }
 531
 532   /**
 533    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 534    * events
 535    */
 536   void addKeyListener()
 537   {
 538     addKeyListener(new KeyAdapter()
 539     {
 540       @Override
 541       public void keyPressed(KeyEvent evt)
 542       {
 543         if (viewport.cursorMode
 544                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 545                         && evt.getKeyCode() <= KeyEvent.VK_9)
 546                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 547                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 548                 && Character.isDigit(evt.getKeyChar()))
 549         {
 550           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 551         }
 552
 553         switch (evt.getKeyCode())
 554         {
 555
 556         case 27: // escape key
 557           deselectAllSequenceMenuItem_actionPerformed(null);
 558
 559           break;
 560
 561         case KeyEvent.VK_DOWN:
 562           if (evt.isAltDown() || !viewport.cursorMode)
 563           {
 564             moveSelectedSequences(false);
 565           }
 566           if (viewport.cursorMode)
 567           {
 568             alignPanel.getSeqPanel().moveCursor(0, 1);
 569           }
 570           break;
 571
 572         case KeyEvent.VK_UP:
 573           if (evt.isAltDown() || !viewport.cursorMode)
 574           {
 575             moveSelectedSequences(true);
 576           }
 577           if (viewport.cursorMode)
 578           {
 579             alignPanel.getSeqPanel().moveCursor(0, -1);
 580           }
 581
 582           break;
 583
 584         case KeyEvent.VK_LEFT:
 585           if (evt.isAltDown() || !viewport.cursorMode)
 586           {
 587             slideSequences(false,
 588                     alignPanel.getSeqPanel().getKeyboardNo1());
 589           }
 590           else
 591           {
 592             alignPanel.getSeqPanel().moveCursor(-1, 0);
 593           }
 594
 595           break;
 596
 597         case KeyEvent.VK_RIGHT:
 598           if (evt.isAltDown() || !viewport.cursorMode)
 599           {
 600             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 601           }
 602           else
 603           {
 604             alignPanel.getSeqPanel().moveCursor(1, 0);
 605           }
 606           break;
 607
 608         case KeyEvent.VK_SPACE:
 609           if (viewport.cursorMode)
 610           {
 611             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 612                     || evt.isShiftDown() || evt.isAltDown());
 613           }
 614           break;
 615
 616         // case KeyEvent.VK_A:
 617         // if (viewport.cursorMode)
 618         // {
 619         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 620         // //System.out.println("A");
 621         // }
 622         // break;
 623         /*
 624          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 625          * System.out.println("closing bracket"); } break;
 626          */
 627         case KeyEvent.VK_DELETE:
 628         case KeyEvent.VK_BACK_SPACE:
 629           if (!viewport.cursorMode)
 630           {
 631             cut_actionPerformed();
 632           }
 633           else
 634           {
 635             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 636                     || evt.isShiftDown() || evt.isAltDown());
 637           }
 638
 639           break;
 640
 641         case KeyEvent.VK_S:
 642           if (viewport.cursorMode)
 643           {
 644             alignPanel.getSeqPanel().setCursorRow();
 645           }
 646           break;
 647         case KeyEvent.VK_C:
 648           if (viewport.cursorMode && !evt.isControlDown())
 649           {
 650             alignPanel.getSeqPanel().setCursorColumn();
 651           }
 652           break;
 653         case KeyEvent.VK_P:
 654           if (viewport.cursorMode)
 655           {
 656             alignPanel.getSeqPanel().setCursorPosition();
 657           }
 658           break;
 659
 660         case KeyEvent.VK_ENTER:
 661         case KeyEvent.VK_COMMA:
 662           if (viewport.cursorMode)
 663           {
 664             alignPanel.getSeqPanel().setCursorRowAndColumn();
 665           }
 666           break;
 667
 668         case KeyEvent.VK_Q:
 669           if (viewport.cursorMode)
 670           {
 671             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 672           }
 673           break;
 674         case KeyEvent.VK_M:
 675           if (viewport.cursorMode)
 676           {
 677             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 678           }
 679           break;
 680
 681         case KeyEvent.VK_F2:
 682           viewport.cursorMode = !viewport.cursorMode;
 683           setStatus(MessageManager
 684                   .formatMessage("label.keyboard_editing_mode", new String[]
 685                   { (viewport.cursorMode ? "on" : "off") }));
 686           if (viewport.cursorMode)
 687           {
 688             ViewportRanges ranges = viewport.getRanges();
 689             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 690                     .getStartRes();
 691             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 692                     .getStartSeq();
 693           }
 694           alignPanel.getSeqPanel().seqCanvas.repaint();
 695           break;
 696
 697         case KeyEvent.VK_F1:
 698           try
 699           {
 700             Help.showHelpWindow();
 701           } catch (Exception ex)
 702           {
 703             ex.printStackTrace();
 704           }
 705           break;
 706         case KeyEvent.VK_H:
 707         {
 708           boolean toggleSeqs = !evt.isControlDown();
 709           boolean toggleCols = !evt.isShiftDown();
 710           toggleHiddenRegions(toggleSeqs, toggleCols);
 711           break;
 712         }
 713         case KeyEvent.VK_B:
 714         {
 715           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 716           boolean modifyExisting = true; // always modify, don't clear
 717                                          // evt.isShiftDown();
 718           boolean invertHighlighted = evt.isAltDown();
 719           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 720                   toggleSel);
 721           break;
 722         }
 723         case KeyEvent.VK_PAGE_UP:
 724           viewport.getRanges().pageUp();
 725           break;
 726         case KeyEvent.VK_PAGE_DOWN:
 727           viewport.getRanges().pageDown();
 728           break;
 729         }
 730       }
 731
 732       @Override
 733       public void keyReleased(KeyEvent evt)
 734       {
 735         switch (evt.getKeyCode())
 736         {
 737         case KeyEvent.VK_LEFT:
 738           if (evt.isAltDown() || !viewport.cursorMode)
 739           {
 740             viewport.firePropertyChange("alignment", null,
 741                     viewport.getAlignment().getSequences());
 742           }
 743           break;
 744
 745         case KeyEvent.VK_RIGHT:
 746           if (evt.isAltDown() || !viewport.cursorMode)
 747           {
 748             viewport.firePropertyChange("alignment", null,
 749                     viewport.getAlignment().getSequences());
 750           }
 751           break;
 752         }
 753       }
 754     });
 755   }
 756
 757   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 758   {
 759     ap.alignFrame = this;
 760     avc = new jalview.controller.AlignViewController(this, viewport,
 761             alignPanel);
 762
 763     alignPanels.add(ap);
 764
 765     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 766
 767     int aSize = alignPanels.size();
 768
 769     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 770
 771     if (aSize == 1 && ap.av.getViewName() == null)
 772     {
 773       this.getContentPane().add(ap, BorderLayout.CENTER);
 774     }
 775     else
 776     {
 777       if (aSize == 2)
 778       {
 779         setInitialTabVisible();
 780       }
 781
 782       expandViews.setEnabled(true);
 783       gatherViews.setEnabled(true);
 784       tabbedPane.addTab(ap.av.getViewName(), ap);
 785
 786       ap.setVisible(false);
 787     }
 788
 789     if (newPanel)
 790     {
 791       if (ap.av.isPadGaps())
 792       {
 793         ap.av.getAlignment().padGaps();
 794       }
 795       ap.av.updateConservation(ap);
 796       ap.av.updateConsensus(ap);
 797       ap.av.updateStrucConsensus(ap);
 798     }
 799   }
 800
 801   public void setInitialTabVisible()
 802   {
 803     expandViews.setEnabled(true);
 804     gatherViews.setEnabled(true);
 805     tabbedPane.setVisible(true);
 806     AlignmentPanel first = alignPanels.get(0);
 807     tabbedPane.addTab(first.av.getViewName(), first);
 808     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 809   }
 810
 811   public AlignViewport getViewport()
 812   {
 813     return viewport;
 814   }
 815
 816   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 817   private void addServiceListeners()
 818   {
 819     final java.beans.PropertyChangeListener thisListener;
 820     Desktop.instance.addJalviewPropertyChangeListener("services",
 821             thisListener = new java.beans.PropertyChangeListener()
 822             {
 823               @Override
 824               public void propertyChange(PropertyChangeEvent evt)
 825               {
 826                 // // System.out.println("Discoverer property change.");
 827                 // if (evt.getPropertyName().equals("services"))
 828                 {
 829                   SwingUtilities.invokeLater(new Runnable()
 830                   {
 831
 832                     @Override
 833                     public void run()
 834                     {
 835                       System.err.println(
 836                               "Rebuild WS Menu for service change");
 837                       BuildWebServiceMenu();
 838                     }
 839
 840                   });
 841                 }
 842               }
 843             });
 844     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 845     {
 846       @Override
 847       public void internalFrameClosed(
 848               javax.swing.event.InternalFrameEvent evt)
 849       {
 850         // System.out.println("deregistering discoverer listener");
 851         Desktop.instance.removeJalviewPropertyChangeListener("services",
 852                 thisListener);
 853         closeMenuItem_actionPerformed(true);
 854       }
 855     });
 856     // Finally, build the menu once to get current service state
 857     new Thread(new Runnable()
 858     {
 859       @Override
 860       public void run()
 861       {
 862         BuildWebServiceMenu();
 863       }
 864     }).start();
 865   }
 866
 867   /**
 868    * Configure menu items that vary according to whether the alignment is
 869    * nucleotide or protein
 870    */
 871   public void setGUINucleotide()
 872   {
 873     AlignmentI al = getViewport().getAlignment();
 874     boolean nucleotide = al.isNucleotide();
 875
 876     loadVcf.setVisible(nucleotide);
 877     showTranslation.setVisible(nucleotide);
 878     showReverse.setVisible(nucleotide);
 879     showReverseComplement.setVisible(nucleotide);
 880     conservationMenuItem.setEnabled(!nucleotide);
 881     modifyConservation
 882             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 883     showGroupConservation.setEnabled(!nucleotide);
 884
 885     showComplementMenuItem
 886             .setText(nucleotide ? MessageManager.getString("label.protein")
 887                     : MessageManager.getString("label.nucleotide"));
 888   }
 889
 890   /**
 891    * set up menus for the current viewport. This may be called after any
 892    * operation that affects the data in the current view (selection changed,
 893    * etc) to update the menus to reflect the new state.
 894    */
 895   @Override
 896   public void setMenusForViewport()
 897   {
 898     setMenusFromViewport(viewport);
 899   }
 900
 901   /**
 902    * Need to call this method when tabs are selected for multiple views, or when
 903    * loading from Jalview2XML.java
 904    *
 905    * @param av
 906    *          AlignViewport
 907    */
 908   public void setMenusFromViewport(AlignViewport av)
 909   {
 910     padGapsMenuitem.setSelected(av.isPadGaps());
 911     colourTextMenuItem.setSelected(av.isShowColourText());
 912     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 913     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 914     conservationMenuItem.setSelected(av.getConservationSelected());
 915     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 916     seqLimits.setSelected(av.getShowJVSuffix());
 917     idRightAlign.setSelected(av.isRightAlignIds());
 918     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 919     renderGapsMenuItem.setSelected(av.isRenderGaps());
 920     wrapMenuItem.setSelected(av.getWrapAlignment());
 921     scaleAbove.setVisible(av.getWrapAlignment());
 922     scaleLeft.setVisible(av.getWrapAlignment());
 923     scaleRight.setVisible(av.getWrapAlignment());
 924     annotationPanelMenuItem.setState(av.isShowAnnotation());
 925     /*
 926      * Show/hide annotations only enabled if annotation panel is shown
 927      */
 928     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 929     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 930     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 931     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 932     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 933     viewTextMenuItem.setSelected(av.getShowText());
 934     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 935     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 936     showGroupConservation.setSelected(av.isShowGroupConservation());
 937     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 938     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 939     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 940
 941     ColourMenuHelper.setColourSelected(colourMenu,
 942             av.getGlobalColourScheme());
 943
 944     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 945     hiddenMarkers.setState(av.getShowHiddenMarkers());
 946     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 947     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 948     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 949     autoCalculate.setSelected(av.autoCalculateConsensus);
 950     sortByTree.setSelected(av.sortByTree);
 951     listenToViewSelections.setSelected(av.followSelection);
 952
 953     showProducts.setEnabled(canShowProducts());
 954     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 955
 956     updateEditMenuBar();
 957   }
 958
 959   /**
 960    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 961    *
 962    * @param b
 963    */
 964   public void setGroovyEnabled(boolean b)
 965   {
 966     runGroovy.setEnabled(b);
 967   }
 968
 969   private IProgressIndicator progressBar;
 970
 971   /*
 972    * (non-Javadoc)
 973    *
 974    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 975    */
 976   @Override
 977   public void setProgressBar(String message, long id)
 978   {
 979     progressBar.setProgressBar(message, id);
 980   }
 981
 982   @Override
 983   public void registerHandler(final long id,
 984           final IProgressIndicatorHandler handler)
 985   {
 986     progressBar.registerHandler(id, handler);
 987   }
 988
 989   /**
 990    *
 991    * @return true if any progress bars are still active
 992    */
 993   @Override
 994   public boolean operationInProgress()
 995   {
 996     return progressBar.operationInProgress();
 997   }
 998
 999   /**
1000    * Sets the text of the status bar. Note that setting a null or empty value
1001    * will cause the status bar to be hidden, with possibly undesirable flicker
1002    * of the screen layout.
1003    */
1004   @Override
1005   public void setStatus(String text)
1006   {
1007     statusBar.setText(text == null || text.isEmpty() ? " " : 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()
1025   {
1026     new 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 = HttpUtils.startsWithHttpOrHttps(fileName)
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
1077         AlignFrame newframe = null;
1078
1079         if (fileObject == null)
1080         {
1081
1082           DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
1083                   ? DataSourceType.URL
1084                   : DataSourceType.FILE;
1085           newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1086                   currentFileFormat);
1087         }
1088         else
1089         {
1090           newframe = loader.LoadFileWaitTillLoaded(fileObject,
1091                   DataSourceType.FILE, currentFileFormat);
1092         }
1093
1094         newframe.setBounds(bounds);
1095         if (featureSettings != null && featureSettings.isShowing())
1096         {
1097           final Rectangle fspos = featureSettings.frame.getBounds();
1098           // TODO: need a 'show feature settings' function that takes bounds -
1099           // need to refactor Desktop.addFrame
1100           newframe.featureSettings_actionPerformed(null);
1101           final FeatureSettings nfs = newframe.featureSettings;
1102           SwingUtilities.invokeLater(new Runnable()
1103           {
1104             @Override
1105             public void run()
1106             {
1107               nfs.frame.setBounds(fspos);
1108             }
1109           });
1110           this.featureSettings.close();
1111           this.featureSettings = null;
1112         }
1113         this.closeMenuItem_actionPerformed(true);
1114       }
1115     }
1116   }
1117
1118   @Override
1119   public void addFromText_actionPerformed(ActionEvent e)
1120   {
1121     Desktop.instance
1122             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1123   }
1124
1125   @Override
1126   public void addFromURL_actionPerformed(ActionEvent e)
1127   {
1128     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1129   }
1130
1131   @Override
1132   public void save_actionPerformed(ActionEvent e)
1133   {
1134     if (fileName == null || (currentFileFormat == null)
1135             || HttpUtils.startsWithHttpOrHttps(fileName))
1136     {
1137       saveAs_actionPerformed();
1138     }
1139     else
1140     {
1141       saveAlignment(fileName, currentFileFormat);
1142     }
1143   }
1144
1145   /**
1146    * Saves the alignment to a file with a name chosen by the user, if necessary
1147    * warning if a file would be overwritten
1148    */
1149   @Override
1150   public void saveAs_actionPerformed()
1151   {
1152     String format = currentFileFormat == null ? null
1153             : currentFileFormat.getName();
1154     JalviewFileChooser chooser = JalviewFileChooser
1155             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1156
1157     chooser.setFileView(new JalviewFileView());
1158     chooser.setDialogTitle(
1159             MessageManager.getString("label.save_alignment_to_file"));
1160     chooser.setToolTipText(MessageManager.getString("action.save"));
1161
1162     int value = chooser.showSaveDialog(this);
1163
1164     if (value != JalviewFileChooser.APPROVE_OPTION)
1165     {
1166       return;
1167     }
1168     currentFileFormat = chooser.getSelectedFormat();
1169     // todo is this (2005) test now obsolete - value is never null?
1170     while (currentFileFormat == null)
1171     {
1172       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1173               MessageManager
1174                       .getString("label.select_file_format_before_saving"),
1175               MessageManager.getString("label.file_format_not_specified"),
1176               JvOptionPane.WARNING_MESSAGE);
1177       currentFileFormat = chooser.getSelectedFormat();
1178       value = chooser.showSaveDialog(this);
1179       if (value != JalviewFileChooser.APPROVE_OPTION)
1180       {
1181         return;
1182       }
1183     }
1184
1185     fileName = chooser.getSelectedFile().getPath();
1186
1187     Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1188     Cache.setProperty("LAST_DIRECTORY", fileName);
1189     saveAlignment(fileName, currentFileFormat);
1190   }
1191
1192   boolean lastSaveSuccessful = false;
1193
1194   FileFormatI lastFormatSaved;
1195
1196   String lastFilenameSaved;
1197
1198   /**
1199    * Raise a dialog or status message for the last call to saveAlignment.
1200    *
1201    * @return true if last call to saveAlignment(file, format) was successful.
1202    */
1203   public boolean isSaveAlignmentSuccessful()
1204   {
1205
1206     if (!lastSaveSuccessful)
1207     {
1208       if (!Platform.isHeadless())
1209       {
1210         JvOptionPane.showInternalMessageDialog(this, MessageManager
1211                 .formatMessage("label.couldnt_save_file", new Object[]
1212                 { lastFilenameSaved }),
1213                 MessageManager.getString("label.error_saving_file"),
1214                 JvOptionPane.WARNING_MESSAGE);
1215       }
1216       else
1217       {
1218         Cache.log.error(MessageManager
1219                 .formatMessage("label.couldnt_save_file", new Object[]
1220                 { lastFilenameSaved }));
1221       }
1222     }
1223     else
1224     {
1225
1226       setStatus(MessageManager.formatMessage(
1227               "label.successfully_saved_to_file_in_format", new Object[]
1228               { lastFilenameSaved, lastFormatSaved }));
1229
1230     }
1231     return lastSaveSuccessful;
1232   }
1233
1234   /**
1235    * Saves the alignment to the specified file path, in the specified format,
1236    * which may be an alignment format, or Jalview project format. If the
1237    * alignment has hidden regions, or the format is one capable of including
1238    * non-sequence data (features, annotations, groups), then the user may be
1239    * prompted to specify what to include in the output.
1240    *
1241    * @param file
1242    * @param format
1243    */
1244   public void saveAlignment(String file, FileFormatI format)
1245   {
1246     lastSaveSuccessful = true;
1247     lastFilenameSaved = file;
1248     lastFormatSaved = format;
1249
1250     if (FileFormat.Jalview.equals(format))
1251     {
1252       String shortName = title;
1253       if (shortName.indexOf(File.separatorChar) > -1)
1254       {
1255         shortName = shortName
1256                 .substring(shortName.lastIndexOf(File.separatorChar) + 1);
1257       }
1258       lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
1259               shortName);
1260
1261       statusBar.setText(MessageManager.formatMessage(
1262               "label.successfully_saved_to_file_in_format", new Object[]
1263               { file, format }));
1264
1265       return;
1266     }
1267
1268     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1269     Runnable cancelAction = new Runnable()
1270     {
1271       @Override
1272       public void run()
1273       {
1274         lastSaveSuccessful = false;
1275       }
1276     };
1277     Runnable outputAction = new Runnable()
1278     {
1279       @Override
1280       public void run()
1281       {
1282         // todo defer this to inside formatSequences (or later)
1283         AlignmentExportData exportData = viewport
1284                 .getAlignExportData(options);
1285         String output = new FormatAdapter(alignPanel, options)
1286                 .formatSequences(format, exportData.getAlignment(),
1287                         exportData.getOmitHidden(),
1288                         exportData.getStartEndPostions(),
1289                         viewport.getAlignment().getHiddenColumns());
1290         if (output == null)
1291         {
1292           lastSaveSuccessful = false;
1293         }
1294         else
1295         {
1296           // create backupfiles object and get new temp filename destination
1297           boolean doBackup = BackupFiles.getEnabled();
1298           BackupFiles backupfiles = null;
1299           if (doBackup)
1300           {
1301             Cache.log.trace(
1302                     "ALIGNFRAME making backupfiles object for " + file);
1303             backupfiles = new BackupFiles(file);
1304           }
1305           try
1306           {
1307             String tempFilePath = doBackup ? backupfiles.getTempFilePath()
1308                     : file;
1309             Cache.log.trace("ALIGNFRAME setting PrintWriter");
1310             PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
1311
1312             if (backupfiles != null)
1313             {
1314               Cache.log.trace("ALIGNFRAME about to write to temp file "
1315                       + backupfiles.getTempFilePath());
1316             }
1317
1318             out.print(output);
1319             Cache.log.trace("ALIGNFRAME about to close file");
1320             out.close();
1321             Cache.log.trace("ALIGNFRAME closed file");
1322             AlignFrame.this.setTitle(file);
1323             statusBar.setText(MessageManager.formatMessage(
1324                     "label.successfully_saved_to_file_in_format",
1325                     new Object[]
1326                     { fileName, format.getName() }));
1327             lastSaveSuccessful = true;
1328           } catch (IOException e)
1329           {
1330             lastSaveSuccessful = false;
1331             Cache.log.error(
1332                     "ALIGNFRAME Something happened writing the temp file");
1333             Cache.log.error(e.getMessage());
1334             Cache.log.debug(Cache.getStackTraceString(e));
1335           } catch (Exception ex)
1336           {
1337             lastSaveSuccessful = false;
1338             Cache.log.error(
1339                     "ALIGNFRAME Something unexpected happened writing the temp file");
1340             Cache.log.error(ex.getMessage());
1341             Cache.log.debug(Cache.getStackTraceString(ex));
1342           }
1343
1344           if (doBackup)
1345           {
1346             backupfiles.setWriteSuccess(lastSaveSuccessful);
1347             Cache.log.debug("ALIGNFRAME writing temp file was "
1348                     + (lastSaveSuccessful ? "" : "NOT ") + "successful");
1349             // do the backup file roll and rename the temp file to actual file
1350             Cache.log.trace(
1351                     "ALIGNFRAME about to rollBackupsAndRenameTempFile");
1352             lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
1353             Cache.log.debug(
1354                     "ALIGNFRAME performed rollBackupsAndRenameTempFile "
1355                             + (lastSaveSuccessful ? "" : "un")
1356                             + "successfully");
1357           }
1358         }
1359       }
1360     };
1361
1362     /*
1363      * show dialog with export options if applicable; else just do it
1364      */
1365     if (AlignExportOptions.isNeeded(viewport, format))
1366     {
1367       AlignExportOptions choices = new AlignExportOptions(
1368               alignPanel.getAlignViewport(), format, options);
1369       choices.setResponseAction(0, outputAction);
1370       choices.setResponseAction(1, cancelAction);
1371       choices.showDialog();
1372     }
1373     else
1374     {
1375       outputAction.run();
1376     }
1377   }
1378
1379   /**
1380    * Outputs the alignment to textbox in the requested format, if necessary
1381    * first prompting the user for whether to include hidden regions or
1382    * non-sequence data
1383    *
1384    * @param fileFormatName
1385    */
1386   @Override
1387   protected void outputText_actionPerformed(String fileFormatName)
1388   {
1389     FileFormatI fileFormat = FileFormats.getInstance()
1390             .forName(fileFormatName);
1391     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1392     Runnable outputAction = new Runnable()
1393     {
1394       @Override
1395       public void run()
1396       {
1397         // todo defer this to inside formatSequences (or later)
1398         AlignmentExportData exportData = viewport
1399                 .getAlignExportData(options);
1400         CutAndPasteTransfer cap = new CutAndPasteTransfer();
1401         cap.setForInput(null);
1402         try
1403         {
1404           FileFormatI format = fileFormat;
1405           cap.setText(new FormatAdapter(alignPanel, options)
1406                   .formatSequences(format, exportData.getAlignment(),
1407                           exportData.getOmitHidden(),
1408                           exportData.getStartEndPostions(),
1409                           viewport.getAlignment().getHiddenColumns()));
1410           Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1411                   "label.alignment_output_command", new Object[]
1412                   { fileFormat.getName() }), 600, 500);
1413         } catch (OutOfMemoryError oom)
1414         {
1415           new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1416                   oom);
1417           cap.dispose();
1418         }
1419       }
1420     };
1421
1422     /*
1423      * show dialog with export options if applicable; else just do it
1424      */
1425     if (AlignExportOptions.isNeeded(viewport, fileFormat))
1426     {
1427       AlignExportOptions choices = new AlignExportOptions(
1428               alignPanel.getAlignViewport(), fileFormat, options);
1429       choices.setResponseAction(0, outputAction);
1430       choices.showDialog();
1431     }
1432     else
1433     {
1434       outputAction.run();
1435     }
1436   }
1437
1438   /**
1439    * DOCUMENT ME!
1440    *
1441    * @param e
1442    *          DOCUMENT ME!
1443    */
1444   @Override
1445   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1446   {
1447     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1448     htmlSVG.exportHTML(null);
1449   }
1450
1451   @Override
1452   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1453   {
1454     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1455     bjs.exportHTML(null);
1456   }
1457
1458   public void createImageMap(File file, String image)
1459   {
1460     alignPanel.makePNGImageMap(file, image);
1461   }
1462
1463   /**
1464    * Creates a PNG image of the alignment and writes it to the given file. If
1465    * the file is null, the user is prompted to choose a file.
1466    *
1467    * @param f
1468    */
1469   @Override
1470   public void createPNG(File f)
1471   {
1472     alignPanel.makeAlignmentImage(TYPE.PNG, f);
1473   }
1474
1475   /**
1476    * Creates an EPS image of the alignment and writes it to the given file. If
1477    * the file is null, the user is prompted to choose a file.
1478    *
1479    * @param f
1480    */
1481   @Override
1482   public void createEPS(File f)
1483   {
1484     alignPanel.makeAlignmentImage(TYPE.EPS, f);
1485   }
1486
1487   /**
1488    * Creates an SVG image of the alignment and writes it to the given file. If
1489    * the file is null, the user is prompted to choose a file.
1490    *
1491    * @param f
1492    */
1493   @Override
1494   public void createSVG(File f)
1495   {
1496     alignPanel.makeAlignmentImage(TYPE.SVG, f);
1497   }
1498
1499   @Override
1500   public void pageSetup_actionPerformed(ActionEvent e)
1501   {
1502     PrinterJob printJob = PrinterJob.getPrinterJob();
1503     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1504   }
1505
1506   /**
1507    * DOCUMENT ME!
1508    *
1509    * @param e
1510    *          DOCUMENT ME!
1511    */
1512   @Override
1513   public void printMenuItem_actionPerformed(ActionEvent e)
1514   {
1515     // Putting in a thread avoids Swing painting problems
1516     PrintThread thread = new PrintThread(alignPanel);
1517     thread.start();
1518   }
1519
1520   @Override
1521   public void exportFeatures_actionPerformed(ActionEvent e)
1522   {
1523     new AnnotationExporter(alignPanel).exportFeatures();
1524   }
1525
1526   @Override
1527   public void exportAnnotations_actionPerformed(ActionEvent e)
1528   {
1529     new AnnotationExporter(alignPanel).exportAnnotations();
1530   }
1531
1532   @Override
1533   public void associatedData_actionPerformed(ActionEvent e)
1534   {
1535     final JalviewFileChooser chooser = new JalviewFileChooser(
1536             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1537     chooser.setFileView(new JalviewFileView());
1538     String tooltip = MessageManager
1539             .getString("label.load_jalview_annotations");
1540     chooser.setDialogTitle(tooltip);
1541     chooser.setToolTipText(tooltip);
1542     chooser.setResponseHandler(0, new Runnable()
1543     {
1544       @Override
1545       public void run()
1546       {
1547         String choice = chooser.getSelectedFile().getPath();
1548         jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1549         loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1550       }
1551     });
1552
1553     chooser.showOpenDialog(this);
1554   }
1555
1556   /**
1557    * Close the current view or all views in the alignment frame. If the frame
1558    * only contains one view then the alignment will be removed from memory.
1559    *
1560    * @param closeAllTabs
1561    */
1562   @Override
1563   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1564   {
1565     if (alignPanels != null && alignPanels.size() < 2)
1566     {
1567       closeAllTabs = true;
1568     }
1569
1570     try
1571     {
1572       if (alignPanels != null)
1573       {
1574         if (closeAllTabs)
1575         {
1576           if (this.isClosed())
1577           {
1578             // really close all the windows - otherwise wait till
1579             // setClosed(true) is called
1580             for (int i = 0; i < alignPanels.size(); i++)
1581             {
1582               AlignmentPanel ap = alignPanels.get(i);
1583               ap.closePanel();
1584             }
1585           }
1586         }
1587         else
1588         {
1589           closeView(alignPanel);
1590         }
1591       }
1592       if (closeAllTabs)
1593       {
1594         if (featureSettings != null && featureSettings.isOpen())
1595         {
1596           featureSettings.close();
1597           featureSettings = null;
1598         }
1599         /*
1600          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1601          * be called recursively, with the frame now in 'closed' state
1602          */
1603         this.setClosed(true);
1604       }
1605     } catch (Exception ex)
1606     {
1607       ex.printStackTrace();
1608     }
1609   }
1610
1611   /**
1612    * Close the specified panel and close up tabs appropriately.
1613    *
1614    * @param panelToClose
1615    */
1616   public void closeView(AlignmentPanel panelToClose)
1617   {
1618     int index = tabbedPane.getSelectedIndex();
1619     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1620     alignPanels.remove(panelToClose);
1621     panelToClose.closePanel();
1622     panelToClose = null;
1623
1624     tabbedPane.removeTabAt(closedindex);
1625     tabbedPane.validate();
1626
1627     if (index > closedindex || index == tabbedPane.getTabCount())
1628     {
1629       // modify currently selected tab index if necessary.
1630       index--;
1631     }
1632
1633     this.tabSelectionChanged(index);
1634   }
1635
1636   /**
1637    * DOCUMENT ME!
1638    */
1639   void updateEditMenuBar()
1640   {
1641
1642     if (viewport.getHistoryList().size() > 0)
1643     {
1644       undoMenuItem.setEnabled(true);
1645       CommandI command = viewport.getHistoryList().peek();
1646       undoMenuItem.setText(MessageManager
1647               .formatMessage("label.undo_command", new Object[]
1648               { command.getDescription() }));
1649     }
1650     else
1651     {
1652       undoMenuItem.setEnabled(false);
1653       undoMenuItem.setText(MessageManager.getString("action.undo"));
1654     }
1655
1656     if (viewport.getRedoList().size() > 0)
1657     {
1658       redoMenuItem.setEnabled(true);
1659
1660       CommandI command = viewport.getRedoList().peek();
1661       redoMenuItem.setText(MessageManager
1662               .formatMessage("label.redo_command", new Object[]
1663               { command.getDescription() }));
1664     }
1665     else
1666     {
1667       redoMenuItem.setEnabled(false);
1668       redoMenuItem.setText(MessageManager.getString("action.redo"));
1669     }
1670   }
1671
1672   @Override
1673   public void addHistoryItem(CommandI command)
1674   {
1675     if (command.getSize() > 0)
1676     {
1677       viewport.addToHistoryList(command);
1678       viewport.clearRedoList();
1679       updateEditMenuBar();
1680       viewport.updateHiddenColumns();
1681       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1682       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1683       // viewport.getColumnSelection()
1684       // .getHiddenColumns().size() > 0);
1685     }
1686   }
1687
1688   /**
1689    *
1690    * @return alignment objects for all views
1691    */
1692   AlignmentI[] getViewAlignments()
1693   {
1694     if (alignPanels != null)
1695     {
1696       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1697       int i = 0;
1698       for (AlignmentPanel ap : alignPanels)
1699       {
1700         als[i++] = ap.av.getAlignment();
1701       }
1702       return als;
1703     }
1704     if (viewport != null)
1705     {
1706       return new AlignmentI[] { viewport.getAlignment() };
1707     }
1708     return null;
1709   }
1710
1711   /**
1712    * DOCUMENT ME!
1713    *
1714    * @param e
1715    *          DOCUMENT ME!
1716    */
1717   @Override
1718   protected void undoMenuItem_actionPerformed(ActionEvent e)
1719   {
1720     if (viewport.getHistoryList().isEmpty())
1721     {
1722       return;
1723     }
1724     CommandI command = viewport.getHistoryList().pop();
1725     viewport.addToRedoList(command);
1726     command.undoCommand(getViewAlignments());
1727
1728     AlignmentViewport originalSource = getOriginatingSource(command);
1729     updateEditMenuBar();
1730
1731     if (originalSource != null)
1732     {
1733       if (originalSource != viewport)
1734       {
1735         Cache.log.warn(
1736                 "Implementation worry: mismatch of viewport origin for undo");
1737       }
1738       originalSource.updateHiddenColumns();
1739       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1740       // null
1741       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1742       // viewport.getColumnSelection()
1743       // .getHiddenColumns().size() > 0);
1744       originalSource.firePropertyChange("alignment", null,
1745               originalSource.getAlignment().getSequences());
1746     }
1747   }
1748
1749   /**
1750    * DOCUMENT ME!
1751    *
1752    * @param e
1753    *          DOCUMENT ME!
1754    */
1755   @Override
1756   protected void redoMenuItem_actionPerformed(ActionEvent e)
1757   {
1758     if (viewport.getRedoList().size() < 1)
1759     {
1760       return;
1761     }
1762
1763     CommandI command = viewport.getRedoList().pop();
1764     viewport.addToHistoryList(command);
1765     command.doCommand(getViewAlignments());
1766
1767     AlignmentViewport originalSource = getOriginatingSource(command);
1768     updateEditMenuBar();
1769
1770     if (originalSource != null)
1771     {
1772
1773       if (originalSource != viewport)
1774       {
1775         Cache.log.warn(
1776                 "Implementation worry: mismatch of viewport origin for redo");
1777       }
1778       originalSource.updateHiddenColumns();
1779       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1780       // null
1781       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1782       // viewport.getColumnSelection()
1783       // .getHiddenColumns().size() > 0);
1784       originalSource.firePropertyChange("alignment", null,
1785               originalSource.getAlignment().getSequences());
1786     }
1787   }
1788
1789   AlignmentViewport getOriginatingSource(CommandI command)
1790   {
1791     AlignmentViewport originalSource = null;
1792     // For sequence removal and addition, we need to fire
1793     // the property change event FROM the viewport where the
1794     // original alignment was altered
1795     AlignmentI al = null;
1796     if (command instanceof EditCommand)
1797     {
1798       EditCommand editCommand = (EditCommand) command;
1799       al = editCommand.getAlignment();
1800       List<Component> comps = PaintRefresher.components
1801               .get(viewport.getSequenceSetId());
1802
1803       for (Component comp : comps)
1804       {
1805         if (comp instanceof AlignmentPanel)
1806         {
1807           if (al == ((AlignmentPanel) comp).av.getAlignment())
1808           {
1809             originalSource = ((AlignmentPanel) comp).av;
1810             break;
1811           }
1812         }
1813       }
1814     }
1815
1816     if (originalSource == null)
1817     {
1818       // The original view is closed, we must validate
1819       // the current view against the closed view first
1820       if (al != null)
1821       {
1822         PaintRefresher.validateSequences(al, viewport.getAlignment());
1823       }
1824
1825       originalSource = viewport;
1826     }
1827
1828     return originalSource;
1829   }
1830
1831   /**
1832    * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
1833    * or the sequence under cursor in keyboard mode
1834    *
1835    * @param up
1836    *          or down (if !up)
1837    */
1838   public void moveSelectedSequences(boolean up)
1839   {
1840     SequenceGroup sg = viewport.getSelectionGroup();
1841
1842     if (sg == null)
1843     {
1844       if (viewport.cursorMode)
1845       {
1846         sg = new SequenceGroup();
1847         sg.addSequence(viewport.getAlignment().getSequenceAt(
1848                 alignPanel.getSeqPanel().seqCanvas.cursorY), false);
1849       }
1850       else
1851       {
1852         return;
1853       }
1854     }
1855
1856     if (sg.getSize() < 1)
1857     {
1858       return;
1859     }
1860
1861     // TODO: JAL-3733 - add an event to the undo buffer for this !
1862
1863     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1864             viewport.getHiddenRepSequences(), up);
1865     alignPanel.paintAlignment(true, false);
1866   }
1867
1868   synchronized void slideSequences(boolean right, int size)
1869   {
1870     List<SequenceI> sg = new ArrayList<>();
1871     if (viewport.cursorMode)
1872     {
1873       sg.add(viewport.getAlignment()
1874               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1875     }
1876     else if (viewport.getSelectionGroup() != null
1877             && viewport.getSelectionGroup().getSize() != viewport
1878                     .getAlignment().getHeight())
1879     {
1880       sg = viewport.getSelectionGroup()
1881               .getSequences(viewport.getHiddenRepSequences());
1882     }
1883
1884     if (sg.size() < 1)
1885     {
1886       return;
1887     }
1888
1889     List<SequenceI> invertGroup = new ArrayList<>();
1890
1891     for (SequenceI seq : viewport.getAlignment().getSequences())
1892     {
1893       if (!sg.contains(seq))
1894       {
1895         invertGroup.add(seq);
1896       }
1897     }
1898
1899     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1900
1901     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1902     for (int i = 0; i < invertGroup.size(); i++)
1903     {
1904       seqs2[i] = invertGroup.get(i);
1905     }
1906
1907     SlideSequencesCommand ssc;
1908     if (right)
1909     {
1910       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1911               viewport.getGapCharacter());
1912     }
1913     else
1914     {
1915       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1916               viewport.getGapCharacter());
1917     }
1918
1919     int groupAdjustment = 0;
1920     if (ssc.getGapsInsertedBegin() && right)
1921     {
1922       if (viewport.cursorMode)
1923       {
1924         alignPanel.getSeqPanel().moveCursor(size, 0);
1925       }
1926       else
1927       {
1928         groupAdjustment = size;
1929       }
1930     }
1931     else if (!ssc.getGapsInsertedBegin() && !right)
1932     {
1933       if (viewport.cursorMode)
1934       {
1935         alignPanel.getSeqPanel().moveCursor(-size, 0);
1936       }
1937       else
1938       {
1939         groupAdjustment = -size;
1940       }
1941     }
1942
1943     if (groupAdjustment != 0)
1944     {
1945       viewport.getSelectionGroup().setStartRes(
1946               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1947       viewport.getSelectionGroup().setEndRes(
1948               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1949     }
1950
1951     /*
1952      * just extend the last slide command if compatible; but not if in
1953      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1954      */
1955     boolean appendHistoryItem = false;
1956     Deque<CommandI> historyList = viewport.getHistoryList();
1957     boolean inSplitFrame = getSplitViewContainer() != null;
1958     if (!inSplitFrame && historyList != null && historyList.size() > 0
1959             && historyList.peek() instanceof SlideSequencesCommand)
1960     {
1961       appendHistoryItem = ssc.appendSlideCommand(
1962               (SlideSequencesCommand) historyList.peek());
1963     }
1964
1965     if (!appendHistoryItem)
1966     {
1967       addHistoryItem(ssc);
1968     }
1969
1970     repaint();
1971   }
1972
1973   /**
1974    * DOCUMENT ME!
1975    *
1976    * @param e
1977    *          DOCUMENT ME!
1978    */
1979   @Override
1980   protected void copy_actionPerformed()
1981   {
1982     if (viewport.getSelectionGroup() == null)
1983     {
1984       return;
1985     }
1986     // TODO: preserve the ordering of displayed alignment annotation in any
1987     // internal paste (particularly sequence associated annotation)
1988     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1989     String[] omitHidden = null;
1990
1991     if (viewport.hasHiddenColumns())
1992     {
1993       omitHidden = viewport.getViewAsString(true);
1994     }
1995
1996     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1997             seqs, omitHidden, null);
1998
1999     StringSelection ss = new StringSelection(output);
2000
2001     try
2002     {
2003       jalview.gui.Desktop.internalCopy = true;
2004       // Its really worth setting the clipboard contents
2005       // to empty before setting the large StringSelection!!
2006       Toolkit.getDefaultToolkit().getSystemClipboard()
2007               .setContents(new StringSelection(""), null);
2008
2009       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
2010               Desktop.instance);
2011     } catch (OutOfMemoryError er)
2012     {
2013       new OOMWarning("copying region", er);
2014       return;
2015     }
2016
2017     HiddenColumns hiddenColumns = null;
2018     if (viewport.hasHiddenColumns())
2019     {
2020       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
2021       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
2022
2023       // create new HiddenColumns object with copy of hidden regions
2024       // between startRes and endRes, offset by startRes
2025       hiddenColumns = new HiddenColumns(
2026               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
2027               hiddenCutoff, hiddenOffset);
2028     }
2029
2030     Desktop.jalviewClipboard = new Object[] { seqs,
2031         viewport.getAlignment().getDataset(), hiddenColumns };
2032     setStatus(MessageManager.formatMessage(
2033             "label.copied_sequences_to_clipboard", new Object[]
2034             { Integer.valueOf(seqs.length).toString() }));
2035   }
2036
2037   /**
2038    * DOCUMENT ME!
2039    *
2040    * @param e
2041    *          DOCUMENT ME!
2042    */
2043   @Override
2044   protected void pasteNew_actionPerformed(ActionEvent e)
2045   {
2046     paste(true);
2047   }
2048
2049   /**
2050    * DOCUMENT ME!
2051    *
2052    * @param e
2053    *          DOCUMENT ME!
2054    */
2055   @Override
2056   protected void pasteThis_actionPerformed(ActionEvent e)
2057   {
2058     paste(false);
2059   }
2060
2061   /**
2062    * Paste contents of Jalview clipboard
2063    *
2064    * @param newAlignment
2065    *          true to paste to a new alignment, otherwise add to this.
2066    */
2067   void paste(boolean newAlignment)
2068   {
2069     boolean externalPaste = true;
2070     try
2071     {
2072       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2073       Transferable contents = c.getContents(this);
2074
2075       if (contents == null)
2076       {
2077         return;
2078       }
2079
2080       String str;
2081       FileFormatI format;
2082       try
2083       {
2084         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2085         if (str.length() < 1)
2086         {
2087           return;
2088         }
2089
2090         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2091
2092       } catch (OutOfMemoryError er)
2093       {
2094         new OOMWarning("Out of memory pasting sequences!!", er);
2095         return;
2096       }
2097
2098       SequenceI[] sequences;
2099       boolean annotationAdded = false;
2100       AlignmentI alignment = null;
2101
2102       if (Desktop.jalviewClipboard != null)
2103       {
2104         // The clipboard was filled from within Jalview, we must use the
2105         // sequences
2106         // And dataset from the copied alignment
2107         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2108         // be doubly sure that we create *new* sequence objects.
2109         sequences = new SequenceI[newseq.length];
2110         for (int i = 0; i < newseq.length; i++)
2111         {
2112           sequences[i] = new Sequence(newseq[i]);
2113         }
2114         alignment = new Alignment(sequences);
2115         externalPaste = false;
2116       }
2117       else
2118       {
2119         // parse the clipboard as an alignment.
2120         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2121                 format);
2122         sequences = alignment.getSequencesArray();
2123       }
2124
2125       int alwidth = 0;
2126       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2127       int fgroup = -1;
2128
2129       if (newAlignment)
2130       {
2131
2132         if (Desktop.jalviewClipboard != null)
2133         {
2134           // dataset is inherited
2135           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2136         }
2137         else
2138         {
2139           // new dataset is constructed
2140           alignment.setDataset(null);
2141         }
2142         alwidth = alignment.getWidth() + 1;
2143       }
2144       else
2145       {
2146         AlignmentI pastedal = alignment; // preserve pasted alignment object
2147         // Add pasted sequences and dataset into existing alignment.
2148         alignment = viewport.getAlignment();
2149         alwidth = alignment.getWidth() + 1;
2150         // decide if we need to import sequences from an existing dataset
2151         boolean importDs = Desktop.jalviewClipboard != null
2152                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2153         // importDs==true instructs us to copy over new dataset sequences from
2154         // an existing alignment
2155         Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
2156                                                                       // create
2157         // minimum dataset set
2158
2159         for (int i = 0; i < sequences.length; i++)
2160         {
2161           if (importDs)
2162           {
2163             newDs.addElement(null);
2164           }
2165           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2166           // paste
2167           if (importDs && ds != null)
2168           {
2169             if (!newDs.contains(ds))
2170             {
2171               newDs.setElementAt(ds, i);
2172               ds = new Sequence(ds);
2173               // update with new dataset sequence
2174               sequences[i].setDatasetSequence(ds);
2175             }
2176             else
2177             {
2178               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2179             }
2180           }
2181           else
2182           {
2183             // copy and derive new dataset sequence
2184             sequences[i] = sequences[i].deriveSequence();
2185             alignment.getDataset()
2186                     .addSequence(sequences[i].getDatasetSequence());
2187             // TODO: avoid creation of duplicate dataset sequences with a
2188             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2189           }
2190           alignment.addSequence(sequences[i]); // merges dataset
2191         }
2192         if (newDs != null)
2193         {
2194           newDs.clear(); // tidy up
2195         }
2196         if (alignment.getAlignmentAnnotation() != null)
2197         {
2198           for (AlignmentAnnotation alan : alignment
2199                   .getAlignmentAnnotation())
2200           {
2201             if (alan.graphGroup > fgroup)
2202             {
2203               fgroup = alan.graphGroup;
2204             }
2205           }
2206         }
2207         if (pastedal.getAlignmentAnnotation() != null)
2208         {
2209           // Add any annotation attached to alignment.
2210           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2211           for (int i = 0; i < alann.length; i++)
2212           {
2213             annotationAdded = true;
2214             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2215             {
2216               AlignmentAnnotation newann = new AlignmentAnnotation(
2217                       alann[i]);
2218               if (newann.graphGroup > -1)
2219               {
2220                 if (newGraphGroups.size() <= newann.graphGroup
2221                         || newGraphGroups.get(newann.graphGroup) == null)
2222                 {
2223                   for (int q = newGraphGroups
2224                           .size(); q <= newann.graphGroup; q++)
2225                   {
2226                     newGraphGroups.add(q, null);
2227                   }
2228                   newGraphGroups.set(newann.graphGroup,
2229                           Integer.valueOf(++fgroup));
2230                 }
2231                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2232                         .intValue();
2233               }
2234
2235               newann.padAnnotation(alwidth);
2236               alignment.addAnnotation(newann);
2237             }
2238           }
2239         }
2240       }
2241       if (!newAlignment)
2242       {
2243         // /////
2244         // ADD HISTORY ITEM
2245         //
2246         addHistoryItem(new EditCommand(
2247                 MessageManager.getString("label.add_sequences"),
2248                 Action.PASTE, sequences, 0, alignment.getWidth(),
2249                 alignment));
2250       }
2251       // Add any annotations attached to sequences
2252       for (int i = 0; i < sequences.length; i++)
2253       {
2254         if (sequences[i].getAnnotation() != null)
2255         {
2256           AlignmentAnnotation newann;
2257           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2258           {
2259             annotationAdded = true;
2260             newann = sequences[i].getAnnotation()[a];
2261             newann.adjustForAlignment();
2262             newann.padAnnotation(alwidth);
2263             if (newann.graphGroup > -1)
2264             {
2265               if (newann.graphGroup > -1)
2266               {
2267                 if (newGraphGroups.size() <= newann.graphGroup
2268                         || newGraphGroups.get(newann.graphGroup) == null)
2269                 {
2270                   for (int q = newGraphGroups
2271                           .size(); q <= newann.graphGroup; q++)
2272                   {
2273                     newGraphGroups.add(q, null);
2274                   }
2275                   newGraphGroups.set(newann.graphGroup,
2276                           Integer.valueOf(++fgroup));
2277                 }
2278                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2279                         .intValue();
2280               }
2281             }
2282             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2283             // was
2284             // duplicated
2285             // earlier
2286             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2287                     a);
2288           }
2289         }
2290       }
2291       if (!newAlignment)
2292       {
2293
2294         // propagate alignment changed.
2295         viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
2296         if (annotationAdded)
2297         {
2298           // Duplicate sequence annotation in all views.
2299           AlignmentI[] alview = this.getViewAlignments();
2300           for (int i = 0; i < sequences.length; i++)
2301           {
2302             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2303             if (sann == null)
2304             {
2305               continue;
2306             }
2307             for (int avnum = 0; avnum < alview.length; avnum++)
2308             {
2309               if (alview[avnum] != alignment)
2310               {
2311                 // duplicate in a view other than the one with input focus
2312                 int avwidth = alview[avnum].getWidth() + 1;
2313                 // this relies on sann being preserved after we
2314                 // modify the sequence's annotation array for each duplication
2315                 for (int a = 0; a < sann.length; a++)
2316                 {
2317                   AlignmentAnnotation newann = new AlignmentAnnotation(
2318                           sann[a]);
2319                   sequences[i].addAlignmentAnnotation(newann);
2320                   newann.padAnnotation(avwidth);
2321                   alview[avnum].addAnnotation(newann); // annotation was
2322                   // duplicated earlier
2323                   // TODO JAL-1145 graphGroups are not updated for sequence
2324                   // annotation added to several views. This may cause
2325                   // strangeness
2326                   alview[avnum].setAnnotationIndex(newann, a);
2327                 }
2328               }
2329             }
2330           }
2331           buildSortByAnnotationScoresMenu();
2332         }
2333         viewport.firePropertyChange("alignment", null,
2334                 alignment.getSequences());
2335         if (alignPanels != null)
2336         {
2337           for (AlignmentPanel ap : alignPanels)
2338           {
2339             ap.validateAnnotationDimensions(false);
2340           }
2341         }
2342         else
2343         {
2344           alignPanel.validateAnnotationDimensions(false);
2345         }
2346
2347       }
2348       else
2349       {
2350         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2351                 DEFAULT_HEIGHT);
2352         String newtitle = new String("Copied sequences");
2353
2354         if (Desktop.jalviewClipboard != null
2355                 && Desktop.jalviewClipboard[2] != null)
2356         {
2357           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2358           af.viewport.setHiddenColumns(hc);
2359         }
2360
2361         // >>>This is a fix for the moment, until a better solution is
2362         // found!!<<<
2363         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2364                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2365                         .getFeatureRenderer());
2366
2367         // TODO: maintain provenance of an alignment, rather than just make the
2368         // title a concatenation of operations.
2369         if (!externalPaste)
2370         {
2371           if (title.startsWith("Copied sequences"))
2372           {
2373             newtitle = title;
2374           }
2375           else
2376           {
2377             newtitle = newtitle.concat("- from " + title);
2378           }
2379         }
2380         else
2381         {
2382           newtitle = new String("Pasted sequences");
2383         }
2384
2385         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2386                 DEFAULT_HEIGHT);
2387
2388       }
2389
2390     } catch (Exception ex)
2391     {
2392       ex.printStackTrace();
2393       System.out.println("Exception whilst pasting: " + ex);
2394       // could be anything being pasted in here
2395     }
2396
2397   }
2398
2399   @Override
2400   protected void expand_newalign(ActionEvent e)
2401   {
2402     try
2403     {
2404       AlignmentI alignment = AlignmentUtils
2405               .expandContext(getViewport().getAlignment(), -1);
2406       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2407               DEFAULT_HEIGHT);
2408       String newtitle = new String("Flanking alignment");
2409
2410       if (Desktop.jalviewClipboard != null
2411               && Desktop.jalviewClipboard[2] != null)
2412       {
2413         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2414         af.viewport.setHiddenColumns(hc);
2415       }
2416
2417       // >>>This is a fix for the moment, until a better solution is
2418       // found!!<<<
2419       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2420               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2421                       .getFeatureRenderer());
2422
2423       // TODO: maintain provenance of an alignment, rather than just make the
2424       // title a concatenation of operations.
2425       {
2426         if (title.startsWith("Copied sequences"))
2427         {
2428           newtitle = title;
2429         }
2430         else
2431         {
2432           newtitle = newtitle.concat("- from " + title);
2433         }
2434       }
2435
2436       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2437
2438     } catch (Exception ex)
2439     {
2440       ex.printStackTrace();
2441       System.out.println("Exception whilst pasting: " + ex);
2442       // could be anything being pasted in here
2443     } catch (OutOfMemoryError oom)
2444     {
2445       new OOMWarning("Viewing flanking region of alignment", oom);
2446     }
2447   }
2448
2449   /**
2450    * Action Cut (delete and copy) the selected region
2451    */
2452   @Override
2453   protected void cut_actionPerformed()
2454   {
2455     copy_actionPerformed();
2456     delete_actionPerformed();
2457   }
2458
2459   /**
2460    * Performs menu option to Delete the currently selected region
2461    */
2462   @Override
2463   protected void delete_actionPerformed()
2464   {
2465
2466     SequenceGroup sg = viewport.getSelectionGroup();
2467     if (sg == null)
2468     {
2469       return;
2470     }
2471
2472     Runnable okAction = new Runnable()
2473     {
2474       @Override
2475       public void run()
2476       {
2477         SequenceI[] cut = sg.getSequences()
2478                 .toArray(new SequenceI[sg.getSize()]);
2479
2480         addHistoryItem(new EditCommand(
2481                 MessageManager.getString("label.cut_sequences"), Action.CUT,
2482                 cut, sg.getStartRes(),
2483                 sg.getEndRes() - sg.getStartRes() + 1,
2484                 viewport.getAlignment()));
2485
2486         viewport.setSelectionGroup(null);
2487         viewport.sendSelection();
2488         viewport.getAlignment().deleteGroup(sg);
2489
2490         viewport.firePropertyChange("alignment", null,
2491                 viewport.getAlignment().getSequences());
2492         if (viewport.getAlignment().getHeight() < 1)
2493         {
2494           try
2495           {
2496             AlignFrame.this.setClosed(true);
2497           } catch (Exception ex)
2498           {
2499           }
2500         }
2501       }
2502     };
2503
2504     /*
2505      * If the cut affects all sequences, prompt for confirmation
2506      */
2507     boolean wholeHeight = sg.getSize() == viewport.getAlignment()
2508             .getHeight();
2509     boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2510             + 1) == viewport.getAlignment().getWidth()) ? true : false;
2511     if (wholeHeight && wholeWidth)
2512     {
2513       JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
2514       dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2515       Object[] options = new Object[] {
2516           MessageManager.getString("action.ok"),
2517           MessageManager.getString("action.cancel") };
2518       dialog.showDialog(MessageManager.getString("warn.delete_all"),
2519               MessageManager.getString("label.delete_all"),
2520               JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2521               options, options[0]);
2522     }
2523     else
2524     {
2525       okAction.run();
2526     }
2527   }
2528
2529   /**
2530    * DOCUMENT ME!
2531    *
2532    * @param e
2533    *          DOCUMENT ME!
2534    */
2535   @Override
2536   protected void deleteGroups_actionPerformed(ActionEvent e)
2537   {
2538     if (avc.deleteGroups())
2539     {
2540       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2541       alignPanel.updateAnnotation();
2542       alignPanel.paintAlignment(true, true);
2543     }
2544   }
2545
2546   /**
2547    * DOCUMENT ME!
2548    *
2549    * @param e
2550    *          DOCUMENT ME!
2551    */
2552   @Override
2553   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2554   {
2555     SequenceGroup sg = new SequenceGroup(
2556             viewport.getAlignment().getSequences());
2557
2558     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2559     viewport.setSelectionGroup(sg);
2560     viewport.isSelectionGroupChanged(true);
2561     viewport.sendSelection();
2562     // JAL-2034 - should delegate to
2563     // alignPanel to decide if overview needs
2564     // updating.
2565     alignPanel.paintAlignment(false, false);
2566     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2567   }
2568
2569   /**
2570    * DOCUMENT ME!
2571    *
2572    * @param e
2573    *          DOCUMENT ME!
2574    */
2575   @Override
2576   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2577   {
2578     if (viewport.cursorMode)
2579     {
2580       alignPanel.getSeqPanel().keyboardNo1 = null;
2581       alignPanel.getSeqPanel().keyboardNo2 = null;
2582     }
2583     viewport.setSelectionGroup(null);
2584     viewport.getColumnSelection().clear();
2585     viewport.setSearchResults(null);
2586     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2587     // JAL-2034 - should delegate to
2588     // alignPanel to decide if overview needs
2589     // updating.
2590     alignPanel.paintAlignment(false, false);
2591     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2592     viewport.sendSelection();
2593   }
2594
2595   /**
2596    * DOCUMENT ME!
2597    *
2598    * @param e
2599    *          DOCUMENT ME!
2600    */
2601   @Override
2602   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2603   {
2604     SequenceGroup sg = viewport.getSelectionGroup();
2605
2606     if (sg == null)
2607     {
2608       selectAllSequenceMenuItem_actionPerformed(null);
2609
2610       return;
2611     }
2612
2613     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2614     {
2615       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2616     }
2617     // JAL-2034 - should delegate to
2618     // alignPanel to decide if overview needs
2619     // updating.
2620
2621     alignPanel.paintAlignment(true, false);
2622     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2623     viewport.sendSelection();
2624   }
2625
2626   @Override
2627   public void invertColSel_actionPerformed(ActionEvent e)
2628   {
2629     viewport.invertColumnSelection();
2630     alignPanel.paintAlignment(true, false);
2631     viewport.sendSelection();
2632   }
2633
2634   /**
2635    * DOCUMENT ME!
2636    *
2637    * @param e
2638    *          DOCUMENT ME!
2639    */
2640   @Override
2641   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2642   {
2643     trimAlignment(true);
2644   }
2645
2646   /**
2647    * DOCUMENT ME!
2648    *
2649    * @param e
2650    *          DOCUMENT ME!
2651    */
2652   @Override
2653   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2654   {
2655     trimAlignment(false);
2656   }
2657
2658   void trimAlignment(boolean trimLeft)
2659   {
2660     ColumnSelection colSel = viewport.getColumnSelection();
2661     int column;
2662
2663     if (!colSel.isEmpty())
2664     {
2665       if (trimLeft)
2666       {
2667         column = colSel.getMin();
2668       }
2669       else
2670       {
2671         column = colSel.getMax();
2672       }
2673
2674       SequenceI[] seqs;
2675       if (viewport.getSelectionGroup() != null)
2676       {
2677         seqs = viewport.getSelectionGroup()
2678                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2679       }
2680       else
2681       {
2682         seqs = viewport.getAlignment().getSequencesArray();
2683       }
2684
2685       TrimRegionCommand trimRegion;
2686       if (trimLeft)
2687       {
2688         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2689                 column, viewport.getAlignment());
2690         viewport.getRanges().setStartRes(0);
2691       }
2692       else
2693       {
2694         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2695                 column, viewport.getAlignment());
2696       }
2697
2698       setStatus(MessageManager.formatMessage("label.removed_columns",
2699               new String[]
2700               { Integer.valueOf(trimRegion.getSize()).toString() }));
2701
2702       addHistoryItem(trimRegion);
2703
2704       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2705       {
2706         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2707                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2708         {
2709           viewport.getAlignment().deleteGroup(sg);
2710         }
2711       }
2712
2713       viewport.firePropertyChange("alignment", null,
2714               viewport.getAlignment().getSequences());
2715     }
2716   }
2717
2718   /**
2719    * DOCUMENT ME!
2720    *
2721    * @param e
2722    *          DOCUMENT ME!
2723    */
2724   @Override
2725   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2726   {
2727     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2728
2729     SequenceI[] seqs;
2730     if (viewport.getSelectionGroup() != null)
2731     {
2732       seqs = viewport.getSelectionGroup()
2733               .getSequencesAsArray(viewport.getHiddenRepSequences());
2734       start = viewport.getSelectionGroup().getStartRes();
2735       end = viewport.getSelectionGroup().getEndRes();
2736     }
2737     else
2738     {
2739       seqs = viewport.getAlignment().getSequencesArray();
2740     }
2741
2742     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2743             "Remove Gapped Columns", seqs, start, end,
2744             viewport.getAlignment());
2745
2746     addHistoryItem(removeGapCols);
2747
2748     setStatus(MessageManager.formatMessage("label.removed_empty_columns",
2749             new Object[]
2750             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2751
2752     // This is to maintain viewport position on first residue
2753     // of first sequence
2754     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2755     ViewportRanges ranges = viewport.getRanges();
2756     int startRes = seq.findPosition(ranges.getStartRes());
2757     // ShiftList shifts;
2758     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2759     // edit.alColumnChanges=shifts.getInverse();
2760     // if (viewport.hasHiddenColumns)
2761     // viewport.getColumnSelection().compensateForEdits(shifts);
2762     ranges.setStartRes(seq.findIndex(startRes) - 1);
2763     viewport.firePropertyChange("alignment", null,
2764             viewport.getAlignment().getSequences());
2765
2766   }
2767
2768   /**
2769    * DOCUMENT ME!
2770    *
2771    * @param e
2772    *          DOCUMENT ME!
2773    */
2774   @Override
2775   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2776   {
2777     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2778
2779     SequenceI[] seqs;
2780     if (viewport.getSelectionGroup() != null)
2781     {
2782       seqs = viewport.getSelectionGroup()
2783               .getSequencesAsArray(viewport.getHiddenRepSequences());
2784       start = viewport.getSelectionGroup().getStartRes();
2785       end = viewport.getSelectionGroup().getEndRes();
2786     }
2787     else
2788     {
2789       seqs = viewport.getAlignment().getSequencesArray();
2790     }
2791
2792     // This is to maintain viewport position on first residue
2793     // of first sequence
2794     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2795     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2796
2797     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2798             viewport.getAlignment()));
2799
2800     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2801
2802     viewport.firePropertyChange("alignment", null,
2803             viewport.getAlignment().getSequences());
2804
2805   }
2806
2807   /**
2808    * DOCUMENT ME!
2809    *
2810    * @param e
2811    *          DOCUMENT ME!
2812    */
2813   @Override
2814   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2815   {
2816     viewport.setPadGaps(padGapsMenuitem.isSelected());
2817     viewport.firePropertyChange("alignment", null,
2818             viewport.getAlignment().getSequences());
2819   }
2820
2821   /**
2822    * Opens a Finder dialog
2823    *
2824    * @param e
2825    */
2826   @Override
2827   public void findMenuItem_actionPerformed(ActionEvent e)
2828   {
2829     new Finder(alignPanel);
2830   }
2831
2832   /**
2833    * Create a new view of the current alignment.
2834    */
2835   @Override
2836   public void newView_actionPerformed(ActionEvent e)
2837   {
2838     newView(null, true);
2839   }
2840
2841   /**
2842    * Creates and shows a new view of the current alignment.
2843    *
2844    * @param viewTitle
2845    *          title of newly created view; if null, one will be generated
2846    * @param copyAnnotation
2847    *          if true then duplicate all annnotation, groups and settings
2848    * @return new alignment panel, already displayed.
2849    */
2850   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2851   {
2852     /*
2853      * Create a new AlignmentPanel (with its own, new Viewport)
2854      */
2855     AlignmentPanel newap = new jalview.project.Jalview2XML()
2856             .copyAlignPanel(alignPanel);
2857     if (!copyAnnotation)
2858     {
2859       /*
2860        * remove all groups and annotation except for the automatic stuff
2861        */
2862       newap.av.getAlignment().deleteAllGroups();
2863       newap.av.getAlignment().deleteAllAnnotations(false);
2864     }
2865
2866     newap.av.setGatherViewsHere(false);
2867
2868     if (viewport.getViewName() == null)
2869     {
2870       viewport.setViewName(
2871               MessageManager.getString("label.view_name_original"));
2872     }
2873
2874     /*
2875      * Views share the same edits undo and redo stacks
2876      */
2877     newap.av.setHistoryList(viewport.getHistoryList());
2878     newap.av.setRedoList(viewport.getRedoList());
2879
2880     /*
2881      * copy any visualisation settings that are not saved in the project
2882      */
2883     newap.av.setColourAppliesToAllGroups(
2884             viewport.getColourAppliesToAllGroups());
2885
2886     /*
2887      * Views share the same mappings; need to deregister any new mappings
2888      * created by copyAlignPanel, and register the new reference to the shared
2889      * mappings
2890      */
2891     newap.av.replaceMappings(viewport.getAlignment());
2892
2893     /*
2894      * start up cDNA consensus (if applicable) now mappings are in place
2895      */
2896     if (newap.av.initComplementConsensus())
2897     {
2898       newap.refresh(true); // adjust layout of annotations
2899     }
2900
2901     newap.av.setViewName(getNewViewName(viewTitle));
2902
2903     addAlignmentPanel(newap, true);
2904     newap.alignmentChanged();
2905
2906     if (alignPanels.size() == 2)
2907     {
2908       viewport.setGatherViewsHere(true);
2909     }
2910     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2911     return newap;
2912   }
2913
2914   /**
2915    * Make a new name for the view, ensuring it is unique within the current
2916    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2917    * these now use viewId. Unique view names are still desirable for usability.)
2918    *
2919    * @param viewTitle
2920    * @return
2921    */
2922   protected String getNewViewName(String viewTitle)
2923   {
2924     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2925     boolean addFirstIndex = false;
2926     if (viewTitle == null || viewTitle.trim().length() == 0)
2927     {
2928       viewTitle = MessageManager.getString("action.view");
2929       addFirstIndex = true;
2930     }
2931     else
2932     {
2933       index = 1;// we count from 1 if given a specific name
2934     }
2935     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2936
2937     List<Component> comps = PaintRefresher.components
2938             .get(viewport.getSequenceSetId());
2939
2940     List<String> existingNames = getExistingViewNames(comps);
2941
2942     while (existingNames.contains(newViewName))
2943     {
2944       newViewName = viewTitle + " " + (++index);
2945     }
2946     return newViewName;
2947   }
2948
2949   /**
2950    * Returns a list of distinct view names found in the given list of
2951    * components. View names are held on the viewport of an AlignmentPanel.
2952    *
2953    * @param comps
2954    * @return
2955    */
2956   protected List<String> getExistingViewNames(List<Component> comps)
2957   {
2958     List<String> existingNames = new ArrayList<>();
2959     for (Component comp : comps)
2960     {
2961       if (comp instanceof AlignmentPanel)
2962       {
2963         AlignmentPanel ap = (AlignmentPanel) comp;
2964         if (!existingNames.contains(ap.av.getViewName()))
2965         {
2966           existingNames.add(ap.av.getViewName());
2967         }
2968       }
2969     }
2970     return existingNames;
2971   }
2972
2973   /**
2974    * Explode tabbed views into separate windows.
2975    */
2976   @Override
2977   public void expandViews_actionPerformed(ActionEvent e)
2978   {
2979     Desktop.explodeViews(this);
2980   }
2981
2982   /**
2983    * Gather views in separate windows back into a tabbed presentation.
2984    */
2985   @Override
2986   public void gatherViews_actionPerformed(ActionEvent e)
2987   {
2988     Desktop.instance.gatherViews(this);
2989   }
2990
2991   /**
2992    * DOCUMENT ME!
2993    *
2994    * @param e
2995    *          DOCUMENT ME!
2996    */
2997   @Override
2998   public void font_actionPerformed(ActionEvent e)
2999   {
3000     new FontChooser(alignPanel);
3001   }
3002
3003   /**
3004    * DOCUMENT ME!
3005    *
3006    * @param e
3007    *          DOCUMENT ME!
3008    */
3009   @Override
3010   protected void seqLimit_actionPerformed(ActionEvent e)
3011   {
3012     viewport.setShowJVSuffix(seqLimits.isSelected());
3013
3014     alignPanel.getIdPanel().getIdCanvas()
3015             .setPreferredSize(alignPanel.calculateIdWidth());
3016     alignPanel.paintAlignment(true, false);
3017   }
3018
3019   @Override
3020   public void idRightAlign_actionPerformed(ActionEvent e)
3021   {
3022     viewport.setRightAlignIds(idRightAlign.isSelected());
3023     alignPanel.paintAlignment(false, false);
3024   }
3025
3026   @Override
3027   public void centreColumnLabels_actionPerformed(ActionEvent e)
3028   {
3029     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
3030     alignPanel.paintAlignment(false, false);
3031   }
3032
3033   /*
3034    * (non-Javadoc)
3035    *
3036    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
3037    */
3038   @Override
3039   protected void followHighlight_actionPerformed()
3040   {
3041     /*
3042      * Set the 'follow' flag on the Viewport (and scroll to position if now
3043      * true).
3044      */
3045     final boolean state = this.followHighlightMenuItem.getState();
3046     viewport.setFollowHighlight(state);
3047     if (state)
3048     {
3049       alignPanel.scrollToPosition(viewport.getSearchResults());
3050     }
3051   }
3052
3053   /**
3054    * DOCUMENT ME!
3055    *
3056    * @param e
3057    *          DOCUMENT ME!
3058    */
3059   @Override
3060   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
3061   {
3062     viewport.setColourText(colourTextMenuItem.isSelected());
3063     alignPanel.paintAlignment(false, false);
3064   }
3065
3066   /**
3067    * DOCUMENT ME!
3068    *
3069    * @param e
3070    *          DOCUMENT ME!
3071    */
3072   @Override
3073   public void wrapMenuItem_actionPerformed(ActionEvent e)
3074   {
3075     scaleAbove.setVisible(wrapMenuItem.isSelected());
3076     scaleLeft.setVisible(wrapMenuItem.isSelected());
3077     scaleRight.setVisible(wrapMenuItem.isSelected());
3078     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3079     alignPanel.updateLayout();
3080   }
3081
3082   @Override
3083   public void showAllSeqs_actionPerformed(ActionEvent e)
3084   {
3085     viewport.showAllHiddenSeqs();
3086   }
3087
3088   @Override
3089   public void showAllColumns_actionPerformed(ActionEvent e)
3090   {
3091     viewport.showAllHiddenColumns();
3092     alignPanel.paintAlignment(true, true);
3093     viewport.sendSelection();
3094   }
3095
3096   @Override
3097   public void hideSelSequences_actionPerformed(ActionEvent e)
3098   {
3099     viewport.hideAllSelectedSeqs();
3100   }
3101
3102   /**
3103    * called by key handler and the hide all/show all menu items
3104    *
3105    * @param toggleSeqs
3106    * @param toggleCols
3107    */
3108   protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3109   {
3110
3111     boolean hide = false;
3112     SequenceGroup sg = viewport.getSelectionGroup();
3113     if (!toggleSeqs && !toggleCols)
3114     {
3115       // Hide everything by the current selection - this is a hack - we do the
3116       // invert and then hide
3117       // first check that there will be visible columns after the invert.
3118       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3119               && sg.getStartRes() <= sg.getEndRes()))
3120       {
3121         // now invert the sequence set, if required - empty selection implies
3122         // that no hiding is required.
3123         if (sg != null)
3124         {
3125           invertSequenceMenuItem_actionPerformed(null);
3126           sg = viewport.getSelectionGroup();
3127           toggleSeqs = true;
3128
3129         }
3130         viewport.expandColSelection(sg, true);
3131         // finally invert the column selection and get the new sequence
3132         // selection.
3133         invertColSel_actionPerformed(null);
3134         toggleCols = true;
3135       }
3136     }
3137
3138     if (toggleSeqs)
3139     {
3140       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3141       {
3142         hideSelSequences_actionPerformed(null);
3143         hide = true;
3144       }
3145       else if (!(toggleCols && viewport.hasSelectedColumns()))
3146       {
3147         showAllSeqs_actionPerformed(null);
3148       }
3149     }
3150
3151     if (toggleCols)
3152     {
3153       if (viewport.hasSelectedColumns())
3154       {
3155         hideSelColumns_actionPerformed(null);
3156         if (!toggleSeqs)
3157         {
3158           viewport.setSelectionGroup(sg);
3159         }
3160       }
3161       else if (!hide)
3162       {
3163         showAllColumns_actionPerformed(null);
3164       }
3165     }
3166   }
3167
3168   /*
3169    * (non-Javadoc)
3170    *
3171    * @see
3172    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3173    * event.ActionEvent)
3174    */
3175   @Override
3176   public void hideAllButSelection_actionPerformed(ActionEvent e)
3177   {
3178     toggleHiddenRegions(false, false);
3179     viewport.sendSelection();
3180   }
3181
3182   /*
3183    * (non-Javadoc)
3184    *
3185    * @see
3186    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3187    * .ActionEvent)
3188    */
3189   @Override
3190   public void hideAllSelection_actionPerformed(ActionEvent e)
3191   {
3192     SequenceGroup sg = viewport.getSelectionGroup();
3193     viewport.expandColSelection(sg, false);
3194     viewport.hideAllSelectedSeqs();
3195     viewport.hideSelectedColumns();
3196     alignPanel.updateLayout();
3197     alignPanel.paintAlignment(true, true);
3198     viewport.sendSelection();
3199   }
3200
3201   /*
3202    * (non-Javadoc)
3203    *
3204    * @see
3205    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3206    * ActionEvent)
3207    */
3208   @Override
3209   public void showAllhidden_actionPerformed(ActionEvent e)
3210   {
3211     viewport.showAllHiddenColumns();
3212     viewport.showAllHiddenSeqs();
3213     alignPanel.paintAlignment(true, true);
3214     viewport.sendSelection();
3215   }
3216
3217   @Override
3218   public void hideSelColumns_actionPerformed(ActionEvent e)
3219   {
3220     viewport.hideSelectedColumns();
3221     alignPanel.updateLayout();
3222     alignPanel.paintAlignment(true, true);
3223     viewport.sendSelection();
3224   }
3225
3226   @Override
3227   public void hiddenMarkers_actionPerformed(ActionEvent e)
3228   {
3229     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3230     repaint();
3231   }
3232
3233   /**
3234    * DOCUMENT ME!
3235    *
3236    * @param e
3237    *          DOCUMENT ME!
3238    */
3239   @Override
3240   protected void scaleAbove_actionPerformed(ActionEvent e)
3241   {
3242     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3243     alignPanel.updateLayout();
3244     alignPanel.paintAlignment(true, false);
3245   }
3246
3247   /**
3248    * DOCUMENT ME!
3249    *
3250    * @param e
3251    *          DOCUMENT ME!
3252    */
3253   @Override
3254   protected void scaleLeft_actionPerformed(ActionEvent e)
3255   {
3256     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3257     alignPanel.updateLayout();
3258     alignPanel.paintAlignment(true, false);
3259   }
3260
3261   /**
3262    * DOCUMENT ME!
3263    *
3264    * @param e
3265    *          DOCUMENT ME!
3266    */
3267   @Override
3268   protected void scaleRight_actionPerformed(ActionEvent e)
3269   {
3270     viewport.setScaleRightWrapped(scaleRight.isSelected());
3271     alignPanel.updateLayout();
3272     alignPanel.paintAlignment(true, false);
3273   }
3274
3275   /**
3276    * DOCUMENT ME!
3277    *
3278    * @param e
3279    *          DOCUMENT ME!
3280    */
3281   @Override
3282   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3283   {
3284     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3285     alignPanel.paintAlignment(false, false);
3286   }
3287
3288   /**
3289    * DOCUMENT ME!
3290    *
3291    * @param e
3292    *          DOCUMENT ME!
3293    */
3294   @Override
3295   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3296   {
3297     viewport.setShowText(viewTextMenuItem.isSelected());
3298     alignPanel.paintAlignment(false, false);
3299   }
3300
3301   /**
3302    * DOCUMENT ME!
3303    *
3304    * @param e
3305    *          DOCUMENT ME!
3306    */
3307   @Override
3308   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3309   {
3310     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3311     alignPanel.paintAlignment(false, false);
3312   }
3313
3314   public FeatureSettings featureSettings;
3315
3316   @Override
3317   public FeatureSettingsControllerI getFeatureSettingsUI()
3318   {
3319     return featureSettings;
3320   }
3321
3322   @Override
3323   public void featureSettings_actionPerformed(ActionEvent e)
3324   {
3325     showFeatureSettingsUI();
3326   }
3327
3328   @Override
3329   public FeatureSettingsControllerI showFeatureSettingsUI()
3330   {
3331     if (featureSettings != null)
3332     {
3333       featureSettings.closeOldSettings();
3334       featureSettings = null;
3335     }
3336     if (!showSeqFeatures.isSelected())
3337     {
3338       // make sure features are actually displayed
3339       showSeqFeatures.setSelected(true);
3340       showSeqFeatures_actionPerformed(null);
3341     }
3342     featureSettings = new FeatureSettings(this);
3343     return featureSettings;
3344   }
3345
3346   /**
3347    * Set or clear 'Show Sequence Features'
3348    *
3349    * @param evt
3350    *          DOCUMENT ME!
3351    */
3352   @Override
3353   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3354   {
3355     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3356     alignPanel.paintAlignment(true, true);
3357   }
3358
3359   /**
3360    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3361    * the annotations panel as a whole.
3362    *
3363    * The options to show/hide all annotations should be enabled when the panel
3364    * is shown, and disabled when the panel is hidden.
3365    *
3366    * @param e
3367    */
3368   @Override
3369   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3370   {
3371     final boolean setVisible = annotationPanelMenuItem.isSelected();
3372     viewport.setShowAnnotation(setVisible);
3373     this.showAllSeqAnnotations.setEnabled(setVisible);
3374     this.hideAllSeqAnnotations.setEnabled(setVisible);
3375     this.showAllAlAnnotations.setEnabled(setVisible);
3376     this.hideAllAlAnnotations.setEnabled(setVisible);
3377     alignPanel.updateLayout();
3378   }
3379
3380   @Override
3381   public void alignmentProperties()
3382   {
3383     JComponent pane;
3384     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3385
3386             .formatAsHtml();
3387     String content = MessageManager.formatMessage("label.html_content",
3388             new Object[]
3389             { contents.toString() });
3390     contents = null;
3391
3392     if (Platform.isJS())
3393     {
3394       JLabel textLabel = new JLabel();
3395       textLabel.setText(content);
3396       textLabel.setBackground(Color.WHITE);
3397
3398       pane = new JPanel(new BorderLayout());
3399       ((JPanel) pane).setOpaque(true);
3400       pane.setBackground(Color.WHITE);
3401       ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3402     }
3403     else
3404     /**
3405      * Java only
3406      *
3407      * @j2sIgnore
3408      */
3409     {
3410       JEditorPane editPane = new JEditorPane("text/html", "");
3411       editPane.setEditable(false);
3412       editPane.setText(content);
3413       pane = editPane;
3414     }
3415
3416     JInternalFrame frame = new JInternalFrame();
3417
3418     frame.getContentPane().add(new JScrollPane(pane));
3419
3420     Desktop.addInternalFrame(frame, MessageManager
3421             .formatMessage("label.alignment_properties", new Object[]
3422             { getTitle() }), 500, 400);
3423   }
3424
3425   /**
3426    * DOCUMENT ME!
3427    *
3428    * @param e
3429    *          DOCUMENT ME!
3430    */
3431   @Override
3432   public void overviewMenuItem_actionPerformed(ActionEvent e)
3433   {
3434     if (alignPanel.overviewPanel != null)
3435     {
3436       return;
3437     }
3438
3439     JInternalFrame frame = new JInternalFrame();
3440     final OverviewPanel overview = new OverviewPanel(alignPanel);
3441     frame.setContentPane(overview);
3442     Desktop.addInternalFrame(frame, MessageManager
3443             .formatMessage("label.overview_params", new Object[]
3444             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3445             true, true);
3446     frame.pack();
3447     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3448     frame.addInternalFrameListener(
3449             new javax.swing.event.InternalFrameAdapter()
3450             {
3451               @Override
3452               public void internalFrameClosed(
3453                       javax.swing.event.InternalFrameEvent evt)
3454               {
3455                 overview.dispose();
3456                 alignPanel.setOverviewPanel(null);
3457               }
3458             });
3459     if (getKeyListeners().length > 0)
3460     {
3461       frame.addKeyListener(getKeyListeners()[0]);
3462     }
3463
3464     alignPanel.setOverviewPanel(overview);
3465   }
3466
3467   @Override
3468   public void textColour_actionPerformed()
3469   {
3470     new TextColourChooser().chooseColour(alignPanel, null);
3471   }
3472
3473   /*
3474    * public void covariationColour_actionPerformed() {
3475    * changeColour(new
3476    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3477    * ()[0])); }
3478    */
3479   @Override
3480   public void annotationColour_actionPerformed()
3481   {
3482     new AnnotationColourChooser(viewport, alignPanel);
3483   }
3484
3485   @Override
3486   public void annotationColumn_actionPerformed(ActionEvent e)
3487   {
3488     new AnnotationColumnChooser(viewport, alignPanel);
3489   }
3490
3491   /**
3492    * Action on the user checking or unchecking the option to apply the selected
3493    * colour scheme to all groups. If unchecked, groups may have their own
3494    * independent colour schemes.
3495    *
3496    * @param selected
3497    */
3498   @Override
3499   public void applyToAllGroups_actionPerformed(boolean selected)
3500   {
3501     viewport.setColourAppliesToAllGroups(selected);
3502   }
3503
3504   /**
3505    * Action on user selecting a colour from the colour menu
3506    *
3507    * @param name
3508    *          the name (not the menu item label!) of the colour scheme
3509    */
3510   @Override
3511   public void changeColour_actionPerformed(String name)
3512   {
3513     /*
3514      * 'User Defined' opens a panel to configure or load a
3515      * user-defined colour scheme
3516      */
3517     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3518     {
3519       new UserDefinedColours(alignPanel);
3520       return;
3521     }
3522
3523     /*
3524      * otherwise set the chosen colour scheme (or null for 'None')
3525      */
3526     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3527             viewport, viewport.getAlignment(),
3528             viewport.getHiddenRepSequences());
3529     changeColour(cs);
3530   }
3531
3532   /**
3533    * Actions on setting or changing the alignment colour scheme
3534    *
3535    * @param cs
3536    */
3537   @Override
3538   public void changeColour(ColourSchemeI cs)
3539   {
3540     // TODO: pull up to controller method
3541     ColourMenuHelper.setColourSelected(colourMenu, cs);
3542
3543     viewport.setGlobalColourScheme(cs);
3544
3545     alignPanel.paintAlignment(true, true);
3546   }
3547
3548   /**
3549    * Show the PID threshold slider panel
3550    */
3551   @Override
3552   protected void modifyPID_actionPerformed()
3553   {
3554     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3555             alignPanel.getViewName());
3556     SliderPanel.showPIDSlider();
3557   }
3558
3559   /**
3560    * Show the Conservation slider panel
3561    */
3562   @Override
3563   protected void modifyConservation_actionPerformed()
3564   {
3565     SliderPanel.setConservationSlider(alignPanel,
3566             viewport.getResidueShading(), alignPanel.getViewName());
3567     SliderPanel.showConservationSlider();
3568   }
3569
3570   /**
3571    * Action on selecting or deselecting (Colour) By Conservation
3572    */
3573   @Override
3574   public void conservationMenuItem_actionPerformed(boolean selected)
3575   {
3576     modifyConservation.setEnabled(selected);
3577     viewport.setConservationSelected(selected);
3578     viewport.getResidueShading().setConservationApplied(selected);
3579
3580     changeColour(viewport.getGlobalColourScheme());
3581     if (selected)
3582     {
3583       modifyConservation_actionPerformed();
3584     }
3585     else
3586     {
3587       SliderPanel.hideConservationSlider();
3588     }
3589   }
3590
3591   /**
3592    * Action on selecting or deselecting (Colour) Above PID Threshold
3593    */
3594   @Override
3595   public void abovePIDThreshold_actionPerformed(boolean selected)
3596   {
3597     modifyPID.setEnabled(selected);
3598     viewport.setAbovePIDThreshold(selected);
3599     if (!selected)
3600     {
3601       viewport.getResidueShading().setThreshold(0,
3602               viewport.isIgnoreGapsConsensus());
3603     }
3604
3605     changeColour(viewport.getGlobalColourScheme());
3606     if (selected)
3607     {
3608       modifyPID_actionPerformed();
3609     }
3610     else
3611     {
3612       SliderPanel.hidePIDSlider();
3613     }
3614   }
3615
3616   /**
3617    * DOCUMENT ME!
3618    *
3619    * @param e
3620    *          DOCUMENT ME!
3621    */
3622   @Override
3623   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3624   {
3625     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3626     AlignmentSorter.sortByPID(viewport.getAlignment(),
3627             viewport.getAlignment().getSequenceAt(0));
3628     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3629             viewport.getAlignment()));
3630     alignPanel.paintAlignment(true, false);
3631   }
3632
3633   /**
3634    * DOCUMENT ME!
3635    *
3636    * @param e
3637    *          DOCUMENT ME!
3638    */
3639   @Override
3640   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3641   {
3642     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3643     AlignmentSorter.sortByID(viewport.getAlignment());
3644     addHistoryItem(
3645             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3646     alignPanel.paintAlignment(true, false);
3647   }
3648
3649   /**
3650    * DOCUMENT ME!
3651    *
3652    * @param e
3653    *          DOCUMENT ME!
3654    */
3655   @Override
3656   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3657   {
3658     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3659     AlignmentSorter.sortByLength(viewport.getAlignment());
3660     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3661             viewport.getAlignment()));
3662     alignPanel.paintAlignment(true, false);
3663   }
3664
3665   /**
3666    * DOCUMENT ME!
3667    *
3668    * @param e
3669    *          DOCUMENT ME!
3670    */
3671   @Override
3672   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3673   {
3674     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3675     AlignmentSorter.sortByGroup(viewport.getAlignment());
3676     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3677             viewport.getAlignment()));
3678
3679     alignPanel.paintAlignment(true, false);
3680   }
3681
3682   /**
3683    * DOCUMENT ME!
3684    *
3685    * @param e
3686    *          DOCUMENT ME!
3687    */
3688   @Override
3689   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3690   {
3691     new RedundancyPanel(alignPanel, this);
3692   }
3693
3694   /**
3695    * DOCUMENT ME!
3696    *
3697    * @param e
3698    *          DOCUMENT ME!
3699    */
3700   @Override
3701   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3702   {
3703     if ((viewport.getSelectionGroup() == null)
3704             || (viewport.getSelectionGroup().getSize() < 2))
3705     {
3706       JvOptionPane.showInternalMessageDialog(this,
3707               MessageManager.getString(
3708                       "label.you_must_select_least_two_sequences"),
3709               MessageManager.getString("label.invalid_selection"),
3710               JvOptionPane.WARNING_MESSAGE);
3711     }
3712     else
3713     {
3714       JInternalFrame frame = new JInternalFrame();
3715       frame.setContentPane(new PairwiseAlignPanel(viewport));
3716       Desktop.addInternalFrame(frame,
3717               MessageManager.getString("action.pairwise_alignment"), 600,
3718               500);
3719     }
3720   }
3721
3722   @Override
3723   public void autoCalculate_actionPerformed(ActionEvent e)
3724   {
3725     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3726     if (viewport.autoCalculateConsensus)
3727     {
3728       viewport.firePropertyChange("alignment", null,
3729               viewport.getAlignment().getSequences());
3730     }
3731   }
3732
3733   @Override
3734   public void sortByTreeOption_actionPerformed(ActionEvent e)
3735   {
3736     viewport.sortByTree = sortByTree.isSelected();
3737   }
3738
3739   @Override
3740   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3741   {
3742     viewport.followSelection = listenToViewSelections.isSelected();
3743   }
3744
3745   /**
3746    * Constructs a tree panel and adds it to the desktop
3747    *
3748    * @param type
3749    *          tree type (NJ or AV)
3750    * @param modelName
3751    *          name of score model used to compute the tree
3752    * @param options
3753    *          parameters for the distance or similarity calculation
3754    */
3755   void newTreePanel(String type, String modelName,
3756           SimilarityParamsI options)
3757   {
3758     String frameTitle = "";
3759     TreePanel tp;
3760
3761     boolean onSelection = false;
3762     if (viewport.getSelectionGroup() != null
3763             && viewport.getSelectionGroup().getSize() > 0)
3764     {
3765       SequenceGroup sg = viewport.getSelectionGroup();
3766
3767       /* Decide if the selection is a column region */
3768       for (SequenceI _s : sg.getSequences())
3769       {
3770         if (_s.getLength() < sg.getEndRes())
3771         {
3772           JvOptionPane.showMessageDialog(Desktop.desktop,
3773                   MessageManager.getString(
3774                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3775                   MessageManager.getString(
3776                           "label.sequences_selection_not_aligned"),
3777                   JvOptionPane.WARNING_MESSAGE);
3778
3779           return;
3780         }
3781       }
3782       onSelection = true;
3783     }
3784     else
3785     {
3786       if (viewport.getAlignment().getHeight() < 2)
3787       {
3788         return;
3789       }
3790     }
3791
3792     tp = new TreePanel(alignPanel, type, modelName, options);
3793     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3794
3795     frameTitle += " from ";
3796
3797     if (viewport.getViewName() != null)
3798     {
3799       frameTitle += viewport.getViewName() + " of ";
3800     }
3801
3802     frameTitle += this.title;
3803
3804     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3805   }
3806
3807   /**
3808    * DOCUMENT ME!
3809    *
3810    * @param title
3811    *          DOCUMENT ME!
3812    * @param order
3813    *          DOCUMENT ME!
3814    */
3815   public void addSortByOrderMenuItem(String title,
3816           final AlignmentOrder order)
3817   {
3818     final JMenuItem item = new JMenuItem(MessageManager
3819             .formatMessage("action.by_title_param", new Object[]
3820             { title }));
3821     sort.add(item);
3822     item.addActionListener(new java.awt.event.ActionListener()
3823     {
3824       @Override
3825       public void actionPerformed(ActionEvent e)
3826       {
3827         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3828
3829         // TODO: JBPNote - have to map order entries to curent SequenceI
3830         // pointers
3831         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3832
3833         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3834                 viewport.getAlignment()));
3835
3836         alignPanel.paintAlignment(true, false);
3837       }
3838     });
3839   }
3840
3841   /**
3842    * Add a new sort by annotation score menu item
3843    *
3844    * @param sort
3845    *          the menu to add the option to
3846    * @param scoreLabel
3847    *          the label used to retrieve scores for each sequence on the
3848    *          alignment
3849    */
3850   public void addSortByAnnotScoreMenuItem(JMenu sort,
3851           final String scoreLabel)
3852   {
3853     final JMenuItem item = new JMenuItem(scoreLabel);
3854     sort.add(item);
3855     item.addActionListener(new java.awt.event.ActionListener()
3856     {
3857       @Override
3858       public void actionPerformed(ActionEvent e)
3859       {
3860         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3861         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3862                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3863         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3864                 viewport.getAlignment()));
3865         alignPanel.paintAlignment(true, false);
3866       }
3867     });
3868   }
3869
3870   /**
3871    * last hash for alignment's annotation array - used to minimise cost of
3872    * rebuild.
3873    */
3874   protected int _annotationScoreVectorHash;
3875
3876   /**
3877    * search the alignment and rebuild the sort by annotation score submenu the
3878    * last alignment annotation vector hash is stored to minimize cost of
3879    * rebuilding in subsequence calls.
3880    *
3881    */
3882   @Override
3883   public void buildSortByAnnotationScoresMenu()
3884   {
3885     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3886     {
3887       return;
3888     }
3889
3890     if (viewport.getAlignment().getAlignmentAnnotation()
3891             .hashCode() != _annotationScoreVectorHash)
3892     {
3893       sortByAnnotScore.removeAll();
3894       // almost certainly a quicker way to do this - but we keep it simple
3895       Hashtable<String, String> scoreSorts = new Hashtable<>();
3896       AlignmentAnnotation aann[];
3897       for (SequenceI sqa : viewport.getAlignment().getSequences())
3898       {
3899         aann = sqa.getAnnotation();
3900         for (int i = 0; aann != null && i < aann.length; i++)
3901         {
3902           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3903           {
3904             scoreSorts.put(aann[i].label, aann[i].label);
3905           }
3906         }
3907       }
3908       Enumeration<String> labels = scoreSorts.keys();
3909       while (labels.hasMoreElements())
3910       {
3911         addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement());
3912       }
3913       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3914       scoreSorts.clear();
3915
3916       _annotationScoreVectorHash = viewport.getAlignment()
3917               .getAlignmentAnnotation().hashCode();
3918     }
3919   }
3920
3921   /**
3922    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3923    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3924    * call. Listeners are added to remove the menu item when the treePanel is
3925    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3926    * modified.
3927    */
3928   @Override
3929   public void buildTreeSortMenu()
3930   {
3931     sortByTreeMenu.removeAll();
3932
3933     List<Component> comps = PaintRefresher.components
3934             .get(viewport.getSequenceSetId());
3935     List<TreePanel> treePanels = new ArrayList<>();
3936     for (Component comp : comps)
3937     {
3938       if (comp instanceof TreePanel)
3939       {
3940         treePanels.add((TreePanel) comp);
3941       }
3942     }
3943
3944     if (treePanels.size() < 1)
3945     {
3946       sortByTreeMenu.setVisible(false);
3947       return;
3948     }
3949
3950     sortByTreeMenu.setVisible(true);
3951
3952     for (final TreePanel tp : treePanels)
3953     {
3954       final JMenuItem item = new JMenuItem(tp.getTitle());
3955       item.addActionListener(new java.awt.event.ActionListener()
3956       {
3957         @Override
3958         public void actionPerformed(ActionEvent e)
3959         {
3960           tp.sortByTree_actionPerformed();
3961           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3962
3963         }
3964       });
3965
3966       sortByTreeMenu.add(item);
3967     }
3968   }
3969
3970   public boolean sortBy(AlignmentOrder alorder, String undoname)
3971   {
3972     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3973     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3974     if (undoname != null)
3975     {
3976       addHistoryItem(new OrderCommand(undoname, oldOrder,
3977               viewport.getAlignment()));
3978     }
3979     alignPanel.paintAlignment(true, false);
3980     return true;
3981   }
3982
3983   /**
3984    * Work out whether the whole set of sequences or just the selected set will
3985    * be submitted for multiple alignment.
3986    *
3987    */
3988   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3989   {
3990     // Now, check we have enough sequences
3991     AlignmentView msa = null;
3992
3993     if ((viewport.getSelectionGroup() != null)
3994             && (viewport.getSelectionGroup().getSize() > 1))
3995     {
3996       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3997       // some common interface!
3998       /*
3999        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
4000        * SequenceI[sz = seqs.getSize(false)];
4001        *
4002        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
4003        * seqs.getSequenceAt(i); }
4004        */
4005       msa = viewport.getAlignmentView(true);
4006     }
4007     else if (viewport.getSelectionGroup() != null
4008             && viewport.getSelectionGroup().getSize() == 1)
4009     {
4010       int option = JvOptionPane.showConfirmDialog(this,
4011               MessageManager.getString("warn.oneseq_msainput_selection"),
4012               MessageManager.getString("label.invalid_selection"),
4013               JvOptionPane.OK_CANCEL_OPTION);
4014       if (option == JvOptionPane.OK_OPTION)
4015       {
4016         msa = viewport.getAlignmentView(false);
4017       }
4018     }
4019     else
4020     {
4021       msa = viewport.getAlignmentView(false);
4022     }
4023     return msa;
4024   }
4025
4026   /**
4027    * Decides what is submitted to a secondary structure prediction service: the
4028    * first sequence in the alignment, or in the current selection, or, if the
4029    * alignment is 'aligned' (ie padded with gaps), then the currently selected
4030    * region or the whole alignment. (where the first sequence in the set is the
4031    * one that the prediction will be for).
4032    */
4033   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
4034   {
4035     AlignmentView seqs = null;
4036
4037     if ((viewport.getSelectionGroup() != null)
4038             && (viewport.getSelectionGroup().getSize() > 0))
4039     {
4040       seqs = viewport.getAlignmentView(true);
4041     }
4042     else
4043     {
4044       seqs = viewport.getAlignmentView(false);
4045     }
4046     // limit sequences - JBPNote in future - could spawn multiple prediction
4047     // jobs
4048     // TODO: viewport.getAlignment().isAligned is a global state - the local
4049     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
4050     if (!viewport.getAlignment().isAligned(false))
4051     {
4052       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
4053       // TODO: if seqs.getSequences().length>1 then should really have warned
4054       // user!
4055
4056     }
4057     return seqs;
4058   }
4059
4060   /**
4061    * DOCUMENT ME!
4062    *
4063    * @param e
4064    *          DOCUMENT ME!
4065    */
4066   @Override
4067   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
4068   {
4069     // Pick the tree file
4070     JalviewFileChooser chooser = new JalviewFileChooser(
4071             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
4072     chooser.setFileView(new JalviewFileView());
4073     chooser.setDialogTitle(
4074             MessageManager.getString("label.select_newick_like_tree_file"));
4075     chooser.setToolTipText(
4076             MessageManager.getString("label.load_tree_file"));
4077
4078     chooser.setResponseHandler(0, new Runnable()
4079     {
4080       @Override
4081       public void run()
4082       {
4083         String filePath = chooser.getSelectedFile().getPath();
4084         Cache.setProperty("LAST_DIRECTORY", filePath);
4085         NewickFile fin = null;
4086         try
4087         {
4088           fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
4089                   DataSourceType.FILE));
4090           viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4091         } catch (Exception ex)
4092         {
4093           JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4094                   MessageManager
4095                           .getString("label.problem_reading_tree_file"),
4096                   JvOptionPane.WARNING_MESSAGE);
4097           ex.printStackTrace();
4098         }
4099         if (fin != null && fin.hasWarningMessage())
4100         {
4101           JvOptionPane.showMessageDialog(Desktop.desktop,
4102                   fin.getWarningMessage(),
4103                   MessageManager.getString(
4104                           "label.possible_problem_with_tree_file"),
4105                   JvOptionPane.WARNING_MESSAGE);
4106         }
4107       }
4108     });
4109     chooser.showOpenDialog(this);
4110   }
4111
4112   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4113   {
4114     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4115   }
4116
4117   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4118           int h, int x, int y)
4119   {
4120     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4121   }
4122
4123   /**
4124    * Add a treeviewer for the tree extracted from a Newick file object to the
4125    * current alignment view
4126    *
4127    * @param nf
4128    *          the tree
4129    * @param title
4130    *          tree viewer title
4131    * @param input
4132    *          Associated alignment input data (or null)
4133    * @param w
4134    *          width
4135    * @param h
4136    *          height
4137    * @param x
4138    *          position
4139    * @param y
4140    *          position
4141    * @return TreePanel handle
4142    */
4143   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4144           AlignmentView input, int w, int h, int x, int y)
4145   {
4146     TreePanel tp = null;
4147
4148     try
4149     {
4150       nf.parse();
4151
4152       if (nf.getTree() != null)
4153       {
4154         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4155
4156         tp.setSize(w, h);
4157
4158         if (x > 0 && y > 0)
4159         {
4160           tp.setLocation(x, y);
4161         }
4162
4163         Desktop.addInternalFrame(tp, treeTitle, w, h);
4164       }
4165     } catch (Exception ex)
4166     {
4167       ex.printStackTrace();
4168     }
4169
4170     return tp;
4171   }
4172
4173   private boolean buildingMenu = false;
4174
4175   /**
4176    * Generates menu items and listener event actions for web service clients
4177    *
4178    */
4179   public void BuildWebServiceMenu()
4180   {
4181     while (buildingMenu)
4182     {
4183       try
4184       {
4185         System.err.println("Waiting for building menu to finish.");
4186         Thread.sleep(10);
4187       } catch (Exception e)
4188       {
4189       }
4190     }
4191     final AlignFrame me = this;
4192     buildingMenu = true;
4193     new Thread(new Runnable()
4194     {
4195       @Override
4196       public void run()
4197       {
4198         final List<JMenuItem> legacyItems = new ArrayList<>();
4199         try
4200         {
4201           // System.err.println("Building ws menu again "
4202           // + Thread.currentThread());
4203           // TODO: add support for context dependent disabling of services based
4204           // on
4205           // alignment and current selection
4206           // TODO: add additional serviceHandle parameter to specify abstract
4207           // handler
4208           // class independently of AbstractName
4209           // TODO: add in rediscovery GUI function to restart discoverer
4210           // TODO: group services by location as well as function and/or
4211           // introduce
4212           // object broker mechanism.
4213           final Vector<JMenu> wsmenu = new Vector<>();
4214           final IProgressIndicator af = me;
4215
4216           /*
4217            * do not i18n these strings - they are hard-coded in class
4218            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4219            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4220            */
4221           final JMenu msawsmenu = new JMenu("Alignment");
4222           final JMenu secstrmenu = new JMenu(
4223                   "Secondary Structure Prediction");
4224           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4225           final JMenu analymenu = new JMenu("Analysis");
4226           final JMenu dismenu = new JMenu("Protein Disorder");
4227           // JAL-940 - only show secondary structure prediction services from
4228           // the legacy server
4229           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4230               // &&
4231           Discoverer.services != null && (Discoverer.services.size() > 0))
4232           {
4233             // TODO: refactor to allow list of AbstractName/Handler bindings to
4234             // be
4235             // stored or retrieved from elsewhere
4236             // No MSAWS used any more:
4237             // Vector msaws = null; // (Vector)
4238             // Discoverer.services.get("MsaWS");
4239             Vector<ServiceHandle> secstrpr = Discoverer.services
4240                     .get("SecStrPred");
4241             if (secstrpr != null)
4242             {
4243               // Add any secondary structure prediction services
4244               for (int i = 0, j = secstrpr.size(); i < j; i++)
4245               {
4246                 final ext.vamsas.ServiceHandle sh = secstrpr.get(i);
4247                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4248                         .getServiceClient(sh);
4249                 int p = secstrmenu.getItemCount();
4250                 impl.attachWSMenuEntry(secstrmenu, me);
4251                 int q = secstrmenu.getItemCount();
4252                 for (int litm = p; litm < q; litm++)
4253                 {
4254                   legacyItems.add(secstrmenu.getItem(litm));
4255                 }
4256               }
4257             }
4258           }
4259
4260           // Add all submenus in the order they should appear on the web
4261           // services menu
4262           wsmenu.add(msawsmenu);
4263           wsmenu.add(secstrmenu);
4264           wsmenu.add(dismenu);
4265           wsmenu.add(analymenu);
4266           // No search services yet
4267           // wsmenu.add(seqsrchmenu);
4268
4269           javax.swing.SwingUtilities.invokeLater(new Runnable()
4270           {
4271             @Override
4272             public void run()
4273             {
4274               try
4275               {
4276                 webService.removeAll();
4277                 // first, add discovered services onto the webservices menu
4278                 if (wsmenu.size() > 0)
4279                 {
4280                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4281                   {
4282                     webService.add(wsmenu.get(i));
4283                   }
4284                 }
4285                 else
4286                 {
4287                   webService.add(me.webServiceNoServices);
4288                 }
4289                 // TODO: move into separate menu builder class.
4290                 boolean new_sspred = false;
4291                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4292                 {
4293                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4294                   if (jws2servs != null)
4295                   {
4296                     if (jws2servs.hasServices())
4297                     {
4298                       jws2servs.attachWSMenuEntry(webService, me);
4299                       for (Jws2Instance sv : jws2servs.getServices())
4300                       {
4301                         if (sv.description.toLowerCase().contains("jpred"))
4302                         {
4303                           for (JMenuItem jmi : legacyItems)
4304                           {
4305                             jmi.setVisible(false);
4306                           }
4307                         }
4308                       }
4309
4310                     }
4311                     if (jws2servs.isRunning())
4312                     {
4313                       JMenuItem tm = new JMenuItem(
4314                               "Still discovering JABA Services");
4315                       tm.setEnabled(false);
4316                       webService.add(tm);
4317                     }
4318                   }
4319                 }
4320                 build_urlServiceMenu(me.webService);
4321                 build_fetchdbmenu(webService);
4322                 for (JMenu item : wsmenu)
4323                 {
4324                   if (item.getItemCount() == 0)
4325                   {
4326                     item.setEnabled(false);
4327                   }
4328                   else
4329                   {
4330                     item.setEnabled(true);
4331                   }
4332                 }
4333               } catch (Exception e)
4334               {
4335                 Cache.log.debug(
4336                         "Exception during web service menu building process.",
4337                         e);
4338               }
4339             }
4340           });
4341         } catch (Exception e)
4342         {
4343         }
4344         buildingMenu = false;
4345       }
4346     }).start();
4347
4348   }
4349
4350   /**
4351    * construct any groupURL type service menu entries.
4352    *
4353    * @param webService
4354    */
4355   protected void build_urlServiceMenu(JMenu webService)
4356   {
4357     // TODO: remove this code when 2.7 is released
4358     // DEBUG - alignmentView
4359     /*
4360      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4361      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4362      *
4363      * @Override public void actionPerformed(ActionEvent e) {
4364      * jalview.datamodel.AlignmentView
4365      * .testSelectionViews(af.viewport.getAlignment(),
4366      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4367      *
4368      * }); webService.add(testAlView);
4369      */
4370     // TODO: refactor to RestClient discoverer and merge menu entries for
4371     // rest-style services with other types of analysis/calculation service
4372     // SHmmr test client - still being implemented.
4373     // DEBUG - alignmentView
4374
4375     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4376             .getRestClients())
4377     {
4378       client.attachWSMenuEntry(
4379               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4380               this);
4381     }
4382   }
4383
4384   /**
4385    * Searches the alignment sequences for xRefs and builds the Show
4386    * Cross-References menu (formerly called Show Products), with database
4387    * sources for which cross-references are found (protein sources for a
4388    * nucleotide alignment and vice versa)
4389    *
4390    * @return true if Show Cross-references menu should be enabled
4391    */
4392   public boolean canShowProducts()
4393   {
4394     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4395     AlignmentI dataset = viewport.getAlignment().getDataset();
4396
4397     showProducts.removeAll();
4398     final boolean dna = viewport.getAlignment().isNucleotide();
4399
4400     if (seqs == null || seqs.length == 0)
4401     {
4402       // nothing to see here.
4403       return false;
4404     }
4405
4406     boolean showp = false;
4407     try
4408     {
4409       List<String> ptypes = new CrossRef(seqs, dataset)
4410               .findXrefSourcesForSequences(dna);
4411
4412       for (final String source : ptypes)
4413       {
4414         showp = true;
4415         final AlignFrame af = this;
4416         JMenuItem xtype = new JMenuItem(source);
4417         xtype.addActionListener(new ActionListener()
4418         {
4419           @Override
4420           public void actionPerformed(ActionEvent e)
4421           {
4422             showProductsFor(af.viewport.getSequenceSelection(), dna,
4423                     source);
4424           }
4425         });
4426         showProducts.add(xtype);
4427       }
4428       showProducts.setVisible(showp);
4429       showProducts.setEnabled(showp);
4430     } catch (Exception e)
4431     {
4432       Cache.log.warn(
4433               "canShowProducts threw an exception - please report to help@jalview.org",
4434               e);
4435       return false;
4436     }
4437     return showp;
4438   }
4439
4440   /**
4441    * Finds and displays cross-references for the selected sequences (protein
4442    * products for nucleotide sequences, dna coding sequences for peptides).
4443    *
4444    * @param sel
4445    *          the sequences to show cross-references for
4446    * @param dna
4447    *          true if from a nucleotide alignment (so showing proteins)
4448    * @param source
4449    *          the database to show cross-references for
4450    */
4451   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4452           final String source)
4453   {
4454     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4455             .start();
4456   }
4457
4458   /**
4459    * Construct and display a new frame containing the translation of this
4460    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4461    */
4462   @Override
4463   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4464   {
4465     AlignmentI al = null;
4466     try
4467     {
4468       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4469
4470       al = dna.translateCdna(codeTable);
4471     } catch (Exception ex)
4472     {
4473       jalview.bin.Cache.log.error(
4474               "Exception during translation. Please report this !", ex);
4475       final String msg = MessageManager.getString(
4476               "label.error_when_translating_sequences_submit_bug_report");
4477       final String errorTitle = MessageManager
4478               .getString("label.implementation_error")
4479               + MessageManager.getString("label.translation_failed");
4480       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4481               JvOptionPane.ERROR_MESSAGE);
4482       return;
4483     }
4484     if (al == null || al.getHeight() == 0)
4485     {
4486       final String msg = MessageManager.getString(
4487               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4488       final String errorTitle = MessageManager
4489               .getString("label.translation_failed");
4490       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4491               JvOptionPane.WARNING_MESSAGE);
4492     }
4493     else
4494     {
4495       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4496       af.setFileFormat(this.currentFileFormat);
4497       final String newTitle = MessageManager
4498               .formatMessage("label.translation_of_params", new Object[]
4499               { this.getTitle(), codeTable.getId() });
4500       af.setTitle(newTitle);
4501       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4502       {
4503         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4504         viewport.openSplitFrame(af, new Alignment(seqs));
4505       }
4506       else
4507       {
4508         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4509                 DEFAULT_HEIGHT);
4510       }
4511     }
4512   }
4513
4514   /**
4515    * Set the file format
4516    *
4517    * @param format
4518    */
4519   public void setFileFormat(FileFormatI format)
4520   {
4521     this.currentFileFormat = format;
4522   }
4523
4524   /**
4525    * Try to load a features file onto the alignment.
4526    *
4527    * @param file
4528    *          contents or path to retrieve file or a File object
4529    * @param sourceType
4530    *          access mode of file (see jalview.io.AlignFile)
4531    * @return true if features file was parsed correctly.
4532    */
4533   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4534   {
4535     // BH 2018
4536     return avc.parseFeaturesFile(file, sourceType,
4537             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4538
4539   }
4540
4541   @Override
4542   public void refreshFeatureUI(boolean enableIfNecessary)
4543   {
4544     // note - currently this is only still here rather than in the controller
4545     // because of the featureSettings hard reference that is yet to be
4546     // abstracted
4547     if (enableIfNecessary)
4548     {
4549       viewport.setShowSequenceFeatures(true);
4550       showSeqFeatures.setSelected(true);
4551     }
4552
4553   }
4554
4555   @Override
4556   public void dragEnter(DropTargetDragEvent evt)
4557   {
4558   }
4559
4560   @Override
4561   public void dragExit(DropTargetEvent evt)
4562   {
4563   }
4564
4565   @Override
4566   public void dragOver(DropTargetDragEvent evt)
4567   {
4568   }
4569
4570   @Override
4571   public void dropActionChanged(DropTargetDragEvent evt)
4572   {
4573   }
4574
4575   @Override
4576   public void drop(DropTargetDropEvent evt)
4577   {
4578     // JAL-1552 - acceptDrop required before getTransferable call for
4579     // Java's Transferable for native dnd
4580     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4581     Transferable t = evt.getTransferable();
4582
4583     final AlignFrame thisaf = this;
4584     final List<Object> files = new ArrayList<>();
4585     List<DataSourceType> protocols = new ArrayList<>();
4586
4587     try
4588     {
4589       Desktop.transferFromDropTarget(files, protocols, evt, t);
4590     } catch (Exception e)
4591     {
4592       e.printStackTrace();
4593     }
4594     if (files != null)
4595     {
4596       new Thread(new Runnable()
4597       {
4598         @Override
4599         public void run()
4600         {
4601           try
4602           {
4603             // check to see if any of these files have names matching sequences
4604             // in
4605             // the alignment
4606             SequenceIdMatcher idm = new SequenceIdMatcher(
4607                     viewport.getAlignment().getSequencesArray());
4608             /**
4609              * Object[] { String,SequenceI}
4610              */
4611             ArrayList<Object[]> filesmatched = new ArrayList<>();
4612             ArrayList<Object> filesnotmatched = new ArrayList<>();
4613             for (int i = 0; i < files.size(); i++)
4614             {
4615               // BH 2018
4616               Object file = files.get(i);
4617               String fileName = file.toString();
4618               String pdbfn = "";
4619               DataSourceType protocol = (file instanceof File
4620                       ? DataSourceType.FILE
4621                       : FormatAdapter.checkProtocol(fileName));
4622               if (protocol == DataSourceType.FILE)
4623               {
4624                 File fl;
4625                 if (file instanceof File)
4626                 {
4627                   fl = (File) file;
4628                   Platform.cacheFileData(fl);
4629                 }
4630                 else
4631                 {
4632                   fl = new File(fileName);
4633                 }
4634                 pdbfn = fl.getName();
4635               }
4636               else if (protocol == DataSourceType.URL)
4637               {
4638                 URL url = new URL(fileName);
4639                 pdbfn = url.getFile();
4640               }
4641               if (pdbfn.length() > 0)
4642               {
4643                 // attempt to find a match in the alignment
4644                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4645                 int l = 0, c = pdbfn.indexOf(".");
4646                 while (mtch == null && c != -1)
4647                 {
4648                   do
4649                   {
4650                     l = c;
4651                   } while ((c = pdbfn.indexOf(".", l)) > l);
4652                   if (l > -1)
4653                   {
4654                     pdbfn = pdbfn.substring(0, l);
4655                   }
4656                   mtch = idm.findAllIdMatches(pdbfn);
4657                 }
4658                 if (mtch != null)
4659                 {
4660                   FileFormatI type;
4661                   try
4662                   {
4663                     type = new IdentifyFile().identify(file, protocol);
4664                   } catch (Exception ex)
4665                   {
4666                     type = null;
4667                   }
4668                   if (type != null && type.isStructureFile())
4669                   {
4670                     filesmatched.add(new Object[] { file, protocol, mtch });
4671                     continue;
4672                   }
4673                 }
4674                 // File wasn't named like one of the sequences or wasn't a PDB
4675                 // file.
4676                 filesnotmatched.add(file);
4677               }
4678             }
4679             int assocfiles = 0;
4680             if (filesmatched.size() > 0)
4681             {
4682               boolean autoAssociate = Cache
4683                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4684               if (!autoAssociate)
4685               {
4686                 String msg = MessageManager.formatMessage(
4687                         "label.automatically_associate_structure_files_with_sequences_same_name",
4688                         new Object[]
4689                         { Integer.valueOf(filesmatched.size())
4690                                 .toString() });
4691                 String ttl = MessageManager.getString(
4692                         "label.automatically_associate_structure_files_by_name");
4693                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4694                         ttl, JvOptionPane.YES_NO_OPTION);
4695                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4696               }
4697               if (autoAssociate)
4698               {
4699                 for (Object[] fm : filesmatched)
4700                 {
4701                   // try and associate
4702                   // TODO: may want to set a standard ID naming formalism for
4703                   // associating PDB files which have no IDs.
4704                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4705                   {
4706                     PDBEntry pe = new AssociatePdbFileWithSeq()
4707                             .associatePdbWithSeq(fm[0].toString(),
4708                                     (DataSourceType) fm[1], toassoc, false,
4709                                     Desktop.instance);
4710                     if (pe != null)
4711                     {
4712                       System.err.println("Associated file : "
4713                               + (fm[0].toString()) + " with "
4714                               + toassoc.getDisplayId(true));
4715                       assocfiles++;
4716                     }
4717                   }
4718                   // TODO: do we need to update overview ? only if features are
4719                   // shown I guess
4720                   alignPanel.paintAlignment(true, false);
4721                 }
4722               }
4723               else
4724               {
4725                 /*
4726                  * add declined structures as sequences
4727                  */
4728                 for (Object[] o : filesmatched)
4729                 {
4730                   filesnotmatched.add(o[0]);
4731                 }
4732               }
4733             }
4734             if (filesnotmatched.size() > 0)
4735             {
4736               if (assocfiles > 0 && (Cache.getDefault(
4737                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4738                       || JvOptionPane.showConfirmDialog(thisaf,
4739                               "<html>" + MessageManager.formatMessage(
4740                                       "label.ignore_unmatched_dropped_files_info",
4741                                       new Object[]
4742                                       { Integer.valueOf(
4743                                               filesnotmatched.size())
4744                                               .toString() })
4745                                       + "</html>",
4746                               MessageManager.getString(
4747                                       "label.ignore_unmatched_dropped_files"),
4748                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4749               {
4750                 return;
4751               }
4752               for (Object fn : filesnotmatched)
4753               {
4754                 loadJalviewDataFile(fn, null, null, null);
4755               }
4756
4757             }
4758           } catch (Exception ex)
4759           {
4760             ex.printStackTrace();
4761           }
4762         }
4763       }).start();
4764     }
4765   }
4766
4767   /**
4768    * Attempt to load a "dropped" file or URL string, by testing in turn for
4769    * <ul>
4770    * <li>an Annotation file</li>
4771    * <li>a JNet file</li>
4772    * <li>a features file</li>
4773    * <li>else try to interpret as an alignment file</li>
4774    * </ul>
4775    *
4776    * @param file
4777    *          either a filename or a URL string.
4778    */
4779   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4780           FileFormatI format, SequenceI assocSeq)
4781   {
4782     // BH 2018 was String file
4783     try
4784     {
4785       if (sourceType == null)
4786       {
4787         sourceType = FormatAdapter.checkProtocol(file);
4788       }
4789       // if the file isn't identified, or not positively identified as some
4790       // other filetype (PFAM is default unidentified alignment file type) then
4791       // try to parse as annotation.
4792       boolean isAnnotation = (format == null
4793               || FileFormat.Pfam.equals(format))
4794                       ? new AnnotationFile().annotateAlignmentView(viewport,
4795                               file, sourceType)
4796                       : false;
4797
4798       if (!isAnnotation)
4799       {
4800         // first see if its a T-COFFEE score file
4801         TCoffeeScoreFile tcf = null;
4802         try
4803         {
4804           tcf = new TCoffeeScoreFile(file, sourceType);
4805           if (tcf.isValid())
4806           {
4807             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4808             {
4809               buildColourMenu();
4810               changeColour(
4811                       new TCoffeeColourScheme(viewport.getAlignment()));
4812               isAnnotation = true;
4813               setStatus(MessageManager.getString(
4814                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4815             }
4816             else
4817             {
4818               // some problem - if no warning its probable that the ID matching
4819               // process didn't work
4820               JvOptionPane.showMessageDialog(Desktop.desktop,
4821                       tcf.getWarningMessage() == null
4822                               ? MessageManager.getString(
4823                                       "label.check_file_matches_sequence_ids_alignment")
4824                               : tcf.getWarningMessage(),
4825                       MessageManager.getString(
4826                               "label.problem_reading_tcoffee_score_file"),
4827                       JvOptionPane.WARNING_MESSAGE);
4828             }
4829           }
4830           else
4831           {
4832             tcf = null;
4833           }
4834         } catch (Exception x)
4835         {
4836           Cache.log.debug(
4837                   "Exception when processing data source as T-COFFEE score file",
4838                   x);
4839           tcf = null;
4840         }
4841         if (tcf == null)
4842         {
4843           // try to see if its a JNet 'concise' style annotation file *before*
4844           // we
4845           // try to parse it as a features file
4846           if (format == null)
4847           {
4848             format = new IdentifyFile().identify(file, sourceType);
4849           }
4850           if (FileFormat.ScoreMatrix == format)
4851           {
4852             ScoreMatrixFile sm = new ScoreMatrixFile(
4853                     new FileParse(file, sourceType));
4854             sm.parse();
4855             // todo: i18n this message
4856             setStatus(MessageManager.formatMessage(
4857                     "label.successfully_loaded_matrix",
4858                     sm.getMatrixName()));
4859           }
4860           else if (FileFormat.Jnet.equals(format))
4861           {
4862             JPredFile predictions = new JPredFile(file, sourceType);
4863             new JnetAnnotationMaker();
4864             JnetAnnotationMaker.add_annotation(predictions,
4865                     viewport.getAlignment(), 0, false);
4866             viewport.getAlignment().setupJPredAlignment();
4867             isAnnotation = true;
4868           }
4869           // else if (IdentifyFile.FeaturesFile.equals(format))
4870           else if (FileFormat.Features.equals(format))
4871           {
4872             if (parseFeaturesFile(file, sourceType))
4873             {
4874               SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4875               if (splitFrame != null)
4876               {
4877                 splitFrame.repaint();
4878               }
4879               else
4880               {
4881                 alignPanel.paintAlignment(true, true);
4882               }
4883             }
4884           }
4885           else
4886           {
4887             new FileLoader().LoadFile(viewport, file, sourceType, format);
4888           }
4889         }
4890       }
4891       if (isAnnotation)
4892       {
4893
4894         alignPanel.adjustAnnotationHeight();
4895         viewport.updateSequenceIdColours();
4896         buildSortByAnnotationScoresMenu();
4897         alignPanel.paintAlignment(true, true);
4898       }
4899     } catch (Exception ex)
4900     {
4901       ex.printStackTrace();
4902     } catch (OutOfMemoryError oom)
4903     {
4904       try
4905       {
4906         System.gc();
4907       } catch (Exception x)
4908       {
4909       }
4910       new OOMWarning(
4911               "loading data "
4912                       + (sourceType != null
4913                               ? (sourceType == DataSourceType.PASTE
4914                                       ? "from clipboard."
4915                                       : "using " + sourceType + " from "
4916                                               + file)
4917                               : ".")
4918                       + (format != null
4919                               ? "(parsing as '" + format + "' file)"
4920                               : ""),
4921               oom, Desktop.desktop);
4922     }
4923   }
4924
4925   /**
4926    * Method invoked by the ChangeListener on the tabbed pane, in other words
4927    * when a different tabbed pane is selected by the user or programmatically.
4928    */
4929   @Override
4930   public void tabSelectionChanged(int index)
4931   {
4932     if (index > -1)
4933     {
4934       alignPanel = alignPanels.get(index);
4935       viewport = alignPanel.av;
4936       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4937       setMenusFromViewport(viewport);
4938       if (featureSettings != null && featureSettings.isOpen()
4939               && featureSettings.fr.getViewport() != viewport)
4940       {
4941         if (viewport.isShowSequenceFeatures())
4942         {
4943           // refresh the featureSettings to reflect UI change
4944           showFeatureSettingsUI();
4945         }
4946         else
4947         {
4948           // close feature settings for this view.
4949           featureSettings.close();
4950         }
4951       }
4952
4953     }
4954
4955     /*
4956      * 'focus' any colour slider that is open to the selected viewport
4957      */
4958     if (viewport.getConservationSelected())
4959     {
4960       SliderPanel.setConservationSlider(alignPanel,
4961               viewport.getResidueShading(), alignPanel.getViewName());
4962     }
4963     else
4964     {
4965       SliderPanel.hideConservationSlider();
4966     }
4967     if (viewport.getAbovePIDThreshold())
4968     {
4969       SliderPanel.setPIDSliderSource(alignPanel,
4970               viewport.getResidueShading(), alignPanel.getViewName());
4971     }
4972     else
4973     {
4974       SliderPanel.hidePIDSlider();
4975     }
4976
4977     /*
4978      * If there is a frame linked to this one in a SplitPane, switch it to the
4979      * same view tab index. No infinite recursion of calls should happen, since
4980      * tabSelectionChanged() should not get invoked on setting the selected
4981      * index to an unchanged value. Guard against setting an invalid index
4982      * before the new view peer tab has been created.
4983      */
4984     final AlignViewportI peer = viewport.getCodingComplement();
4985     if (peer != null)
4986     {
4987       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4988               .getAlignPanel().alignFrame;
4989       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4990       {
4991         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4992       }
4993     }
4994   }
4995
4996   /**
4997    * On right mouse click on view tab, prompt for and set new view name.
4998    */
4999   @Override
5000   public void tabbedPane_mousePressed(MouseEvent e)
5001   {
5002     if (e.isPopupTrigger())
5003     {
5004       String msg = MessageManager.getString("label.enter_view_name");
5005       String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
5006       String reply = JvOptionPane.showInputDialog(msg, ttl);
5007
5008       if (reply != null)
5009       {
5010         viewport.setViewName(reply);
5011         // TODO warn if reply is in getExistingViewNames()?
5012         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5013       }
5014     }
5015   }
5016
5017   public AlignViewport getCurrentView()
5018   {
5019     return viewport;
5020   }
5021
5022   /**
5023    * Open the dialog for regex description parsing.
5024    */
5025   @Override
5026   protected void extractScores_actionPerformed(ActionEvent e)
5027   {
5028     ParseProperties pp = new jalview.analysis.ParseProperties(
5029             viewport.getAlignment());
5030     // TODO: verify regex and introduce GUI dialog for version 2.5
5031     // if (pp.getScoresFromDescription("col", "score column ",
5032     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5033     // true)>0)
5034     if (pp.getScoresFromDescription("description column",
5035             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5036     {
5037       buildSortByAnnotationScoresMenu();
5038     }
5039   }
5040
5041   /*
5042    * (non-Javadoc)
5043    *
5044    * @see
5045    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5046    * )
5047    */
5048   @Override
5049   protected void showDbRefs_actionPerformed(ActionEvent e)
5050   {
5051     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5052   }
5053
5054   /*
5055    * (non-Javadoc)
5056    *
5057    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5058    * ActionEvent)
5059    */
5060   @Override
5061   protected void showNpFeats_actionPerformed(ActionEvent e)
5062   {
5063     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5064   }
5065
5066   /**
5067    * find the viewport amongst the tabs in this alignment frame and close that
5068    * tab
5069    *
5070    * @param av
5071    */
5072   public boolean closeView(AlignViewportI av)
5073   {
5074     if (viewport == av)
5075     {
5076       this.closeMenuItem_actionPerformed(false);
5077       return true;
5078     }
5079     Component[] comp = tabbedPane.getComponents();
5080     for (int i = 0; comp != null && i < comp.length; i++)
5081     {
5082       if (comp[i] instanceof AlignmentPanel)
5083       {
5084         if (((AlignmentPanel) comp[i]).av == av)
5085         {
5086           // close the view.
5087           closeView((AlignmentPanel) comp[i]);
5088           return true;
5089         }
5090       }
5091     }
5092     return false;
5093   }
5094
5095   protected void build_fetchdbmenu(JMenu webService)
5096   {
5097     // Temporary hack - DBRef Fetcher always top level ws entry.
5098     // TODO We probably want to store a sequence database checklist in
5099     // preferences and have checkboxes.. rather than individual sources selected
5100     // here
5101     final JMenu rfetch = new JMenu(
5102             MessageManager.getString("action.fetch_db_references"));
5103     rfetch.setToolTipText(MessageManager.getString(
5104             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5105     webService.add(rfetch);
5106
5107     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5108             MessageManager.getString("option.trim_retrieved_seqs"));
5109     trimrs.setToolTipText(
5110             MessageManager.getString("label.trim_retrieved_sequences"));
5111     trimrs.setSelected(
5112             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5113     trimrs.addActionListener(new ActionListener()
5114     {
5115       @Override
5116       public void actionPerformed(ActionEvent e)
5117       {
5118         trimrs.setSelected(trimrs.isSelected());
5119         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5120                 Boolean.valueOf(trimrs.isSelected()).toString());
5121       }
5122     });
5123     rfetch.add(trimrs);
5124     JMenuItem fetchr = new JMenuItem(
5125             MessageManager.getString("label.standard_databases"));
5126     fetchr.setToolTipText(
5127             MessageManager.getString("label.fetch_embl_uniprot"));
5128     fetchr.addActionListener(new ActionListener()
5129     {
5130
5131       @Override
5132       public void actionPerformed(ActionEvent e)
5133       {
5134         new Thread(new Runnable()
5135         {
5136           @Override
5137           public void run()
5138           {
5139             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5140                     .getAlignment().isNucleotide();
5141             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5142                     alignPanel.av.getSequenceSelection(),
5143                     alignPanel.alignFrame, null,
5144                     alignPanel.alignFrame.featureSettings, isNucleotide);
5145             dbRefFetcher.addListener(new FetchFinishedListenerI()
5146             {
5147               @Override
5148               public void finished()
5149               {
5150
5151                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5152                         .getFeatureSettingsModels())
5153                 {
5154
5155                   alignPanel.av.mergeFeaturesStyle(srcSettings);
5156                 }
5157                 AlignFrame.this.setMenusForViewport();
5158               }
5159             });
5160             dbRefFetcher.fetchDBRefs(false);
5161           }
5162         }).start();
5163
5164       }
5165
5166     });
5167     rfetch.add(fetchr);
5168     new Thread(new Runnable()
5169     {
5170       @Override
5171       public void run()
5172       {
5173         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5174                 .getSequenceFetcherSingleton();
5175         javax.swing.SwingUtilities.invokeLater(new Runnable()
5176         {
5177           @Override
5178           public void run()
5179           {
5180             String[] dbclasses = sf.getNonAlignmentSources();
5181             List<DbSourceProxy> otherdb;
5182             JMenu dfetch = new JMenu();
5183             JMenu ifetch = new JMenu();
5184             JMenuItem fetchr = null;
5185             int comp = 0, icomp = 0, mcomp = 15;
5186             String mname = null;
5187             int dbi = 0;
5188             for (String dbclass : dbclasses)
5189             {
5190               otherdb = sf.getSourceProxy(dbclass);
5191               // add a single entry for this class, or submenu allowing 'fetch
5192               // all' or pick one
5193               if (otherdb == null || otherdb.size() < 1)
5194               {
5195                 continue;
5196               }
5197               if (mname == null)
5198               {
5199                 mname = "From " + dbclass;
5200               }
5201               if (otherdb.size() == 1)
5202               {
5203                 final DbSourceProxy[] dassource = otherdb
5204                         .toArray(new DbSourceProxy[0]);
5205                 DbSourceProxy src = otherdb.get(0);
5206                 fetchr = new JMenuItem(src.getDbSource());
5207                 fetchr.addActionListener(new ActionListener()
5208                 {
5209
5210                   @Override
5211                   public void actionPerformed(ActionEvent e)
5212                   {
5213                     new Thread(new Runnable()
5214                     {
5215
5216                       @Override
5217                       public void run()
5218                       {
5219                         boolean isNucleotide = alignPanel.alignFrame
5220                                 .getViewport().getAlignment()
5221                                 .isNucleotide();
5222                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5223                                 alignPanel.av.getSequenceSelection(),
5224                                 alignPanel.alignFrame, dassource,
5225                                 alignPanel.alignFrame.featureSettings,
5226                                 isNucleotide);
5227                         dbRefFetcher
5228                                 .addListener(new FetchFinishedListenerI()
5229                                 {
5230                                   @Override
5231                                   public void finished()
5232                                   {
5233                                     FeatureSettingsModelI srcSettings = dassource[0]
5234                                             .getFeatureColourScheme();
5235                                     alignPanel.av.mergeFeaturesStyle(
5236                                             srcSettings);
5237                                     AlignFrame.this.setMenusForViewport();
5238                                   }
5239                                 });
5240                         dbRefFetcher.fetchDBRefs(false);
5241                       }
5242                     }).start();
5243                   }
5244
5245                 });
5246                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5247                         MessageManager.formatMessage(
5248                                 "label.fetch_retrieve_from", new Object[]
5249                                 { src.getDbName() })));
5250                 dfetch.add(fetchr);
5251                 comp++;
5252               }
5253               else
5254               {
5255                 final DbSourceProxy[] dassource = otherdb
5256                         .toArray(new DbSourceProxy[0]);
5257                 // fetch all entry
5258                 DbSourceProxy src = otherdb.get(0);
5259                 fetchr = new JMenuItem(MessageManager
5260                         .formatMessage("label.fetch_all_param", new Object[]
5261                         { src.getDbSource() }));
5262                 fetchr.addActionListener(new ActionListener()
5263                 {
5264                   @Override
5265                   public void actionPerformed(ActionEvent e)
5266                   {
5267                     new Thread(new Runnable()
5268                     {
5269
5270                       @Override
5271                       public void run()
5272                       {
5273                         boolean isNucleotide = alignPanel.alignFrame
5274                                 .getViewport().getAlignment()
5275                                 .isNucleotide();
5276                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5277                                 alignPanel.av.getSequenceSelection(),
5278                                 alignPanel.alignFrame, dassource,
5279                                 alignPanel.alignFrame.featureSettings,
5280                                 isNucleotide);
5281                         dbRefFetcher
5282                                 .addListener(new FetchFinishedListenerI()
5283                                 {
5284                                   @Override
5285                                   public void finished()
5286                                   {
5287                                     AlignFrame.this.setMenusForViewport();
5288                                   }
5289                                 });
5290                         dbRefFetcher.fetchDBRefs(false);
5291                       }
5292                     }).start();
5293                   }
5294                 });
5295
5296                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5297                         MessageManager.formatMessage(
5298                                 "label.fetch_retrieve_from_all_sources",
5299                                 new Object[]
5300                                 { Integer.valueOf(otherdb.size())
5301                                         .toString(),
5302                                     src.getDbSource(), src.getDbName() })));
5303                 dfetch.add(fetchr);
5304                 comp++;
5305                 // and then build the rest of the individual menus
5306                 ifetch = new JMenu(MessageManager.formatMessage(
5307                         "label.source_from_db_source", new Object[]
5308                         { src.getDbSource() }));
5309                 icomp = 0;
5310                 String imname = null;
5311                 int i = 0;
5312                 for (DbSourceProxy sproxy : otherdb)
5313                 {
5314                   String dbname = sproxy.getDbName();
5315                   String sname = dbname.length() > 5
5316                           ? dbname.substring(0, 5) + "..."
5317                           : dbname;
5318                   String msname = dbname.length() > 10
5319                           ? dbname.substring(0, 10) + "..."
5320                           : dbname;
5321                   if (imname == null)
5322                   {
5323                     imname = MessageManager
5324                             .formatMessage("label.from_msname", new Object[]
5325                             { sname });
5326                   }
5327                   fetchr = new JMenuItem(msname);
5328                   final DbSourceProxy[] dassrc = { sproxy };
5329                   fetchr.addActionListener(new ActionListener()
5330                   {
5331
5332                     @Override
5333                     public void actionPerformed(ActionEvent e)
5334                     {
5335                       new Thread(new Runnable()
5336                       {
5337
5338                         @Override
5339                         public void run()
5340                         {
5341                           boolean isNucleotide = alignPanel.alignFrame
5342                                   .getViewport().getAlignment()
5343                                   .isNucleotide();
5344                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5345                                   alignPanel.av.getSequenceSelection(),
5346                                   alignPanel.alignFrame, dassrc,
5347                                   alignPanel.alignFrame.featureSettings,
5348                                   isNucleotide);
5349                           dbRefFetcher
5350                                   .addListener(new FetchFinishedListenerI()
5351                                   {
5352                                     @Override
5353                                     public void finished()
5354                                     {
5355                                       AlignFrame.this.setMenusForViewport();
5356                                     }
5357                                   });
5358                           dbRefFetcher.fetchDBRefs(false);
5359                         }
5360                       }).start();
5361                     }
5362
5363                   });
5364                   fetchr.setToolTipText(
5365                           "<html>" + MessageManager.formatMessage(
5366                                   "label.fetch_retrieve_from", new Object[]
5367                                   { dbname }));
5368                   ifetch.add(fetchr);
5369                   ++i;
5370                   if (++icomp >= mcomp || i == (otherdb.size()))
5371                   {
5372                     ifetch.setText(MessageManager.formatMessage(
5373                             "label.source_to_target", imname, sname));
5374                     dfetch.add(ifetch);
5375                     ifetch = new JMenu();
5376                     imname = null;
5377                     icomp = 0;
5378                     comp++;
5379                   }
5380                 }
5381               }
5382               ++dbi;
5383               if (comp >= mcomp || dbi >= (dbclasses.length))
5384               {
5385                 dfetch.setText(MessageManager.formatMessage(
5386                         "label.source_to_target", mname, dbclass));
5387                 rfetch.add(dfetch);
5388                 dfetch = new JMenu();
5389                 mname = null;
5390                 comp = 0;
5391               }
5392             }
5393           }
5394         });
5395       }
5396     }).start();
5397
5398   }
5399
5400   /**
5401    * Left justify the whole alignment.
5402    */
5403   @Override
5404   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5405   {
5406     AlignmentI al = viewport.getAlignment();
5407     al.justify(false);
5408     viewport.firePropertyChange("alignment", null, al);
5409   }
5410
5411   /**
5412    * Right justify the whole alignment.
5413    */
5414   @Override
5415   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5416   {
5417     AlignmentI al = viewport.getAlignment();
5418     al.justify(true);
5419     viewport.firePropertyChange("alignment", null, al);
5420   }
5421
5422   @Override
5423   public void setShowSeqFeatures(boolean b)
5424   {
5425     showSeqFeatures.setSelected(b);
5426     viewport.setShowSequenceFeatures(b);
5427   }
5428
5429   /*
5430    * (non-Javadoc)
5431    *
5432    * @see
5433    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5434    * awt.event.ActionEvent)
5435    */
5436   @Override
5437   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5438   {
5439     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5440     alignPanel.paintAlignment(false, false);
5441   }
5442
5443   /*
5444    * (non-Javadoc)
5445    *
5446    * @see
5447    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5448    * .ActionEvent)
5449    */
5450   @Override
5451   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5452   {
5453     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5454     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5455
5456   }
5457
5458   /*
5459    * (non-Javadoc)
5460    *
5461    * @see
5462    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5463    * .event.ActionEvent)
5464    */
5465   @Override
5466   protected void showGroupConservation_actionPerformed(ActionEvent e)
5467   {
5468     viewport.setShowGroupConservation(showGroupConservation.getState());
5469     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5470   }
5471
5472   /*
5473    * (non-Javadoc)
5474    *
5475    * @see
5476    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5477    * .event.ActionEvent)
5478    */
5479   @Override
5480   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5481   {
5482     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5483     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5484   }
5485
5486   /*
5487    * (non-Javadoc)
5488    *
5489    * @see
5490    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5491    * .event.ActionEvent)
5492    */
5493   @Override
5494   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5495   {
5496     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5497     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5498   }
5499
5500   @Override
5501   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5502   {
5503     showSequenceLogo.setState(true);
5504     viewport.setShowSequenceLogo(true);
5505     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5506     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5507   }
5508
5509   @Override
5510   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5511   {
5512     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5513   }
5514
5515   /*
5516    * (non-Javadoc)
5517    *
5518    * @see
5519    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5520    * .event.ActionEvent)
5521    */
5522   @Override
5523   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5524   {
5525     if (avc.makeGroupsFromSelection())
5526     {
5527       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5528       alignPanel.updateAnnotation();
5529       alignPanel.paintAlignment(true,
5530               viewport.needToUpdateStructureViews());
5531     }
5532   }
5533
5534   public void clearAlignmentSeqRep()
5535   {
5536     // TODO refactor alignmentseqrep to controller
5537     if (viewport.getAlignment().hasSeqrep())
5538     {
5539       viewport.getAlignment().setSeqrep(null);
5540       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5541       alignPanel.updateAnnotation();
5542       alignPanel.paintAlignment(true, true);
5543     }
5544   }
5545
5546   @Override
5547   protected void createGroup_actionPerformed(ActionEvent e)
5548   {
5549     if (avc.createGroup())
5550     {
5551       if (applyAutoAnnotationSettings.isSelected())
5552       {
5553         alignPanel.updateAnnotation(true, false);
5554       }
5555       alignPanel.alignmentChanged();
5556     }
5557   }
5558
5559   @Override
5560   protected void unGroup_actionPerformed(ActionEvent e)
5561   {
5562     if (avc.unGroup())
5563     {
5564       alignPanel.alignmentChanged();
5565     }
5566   }
5567
5568   /**
5569    * make the given alignmentPanel the currently selected tab
5570    *
5571    * @param alignmentPanel
5572    */
5573   public void setDisplayedView(AlignmentPanel alignmentPanel)
5574   {
5575     if (!viewport.getSequenceSetId()
5576             .equals(alignmentPanel.av.getSequenceSetId()))
5577     {
5578       throw new Error(MessageManager.getString(
5579               "error.implementation_error_cannot_show_view_alignment_frame"));
5580     }
5581     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5582             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5583     {
5584       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5585     }
5586   }
5587
5588   /**
5589    * Action on selection of menu options to Show or Hide annotations.
5590    *
5591    * @param visible
5592    * @param forSequences
5593    *          update sequence-related annotations
5594    * @param forAlignment
5595    *          update non-sequence-related annotations
5596    */
5597   @Override
5598   protected void setAnnotationsVisibility(boolean visible,
5599           boolean forSequences, boolean forAlignment)
5600   {
5601     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5602             .getAlignmentAnnotation();
5603     if (anns == null)
5604     {
5605       return;
5606     }
5607     for (AlignmentAnnotation aa : anns)
5608     {
5609       /*
5610        * don't display non-positional annotations on an alignment
5611        */
5612       if (aa.annotations == null)
5613       {
5614         continue;
5615       }
5616       boolean apply = (aa.sequenceRef == null && forAlignment)
5617               || (aa.sequenceRef != null && forSequences);
5618       if (apply)
5619       {
5620         aa.visible = visible;
5621       }
5622     }
5623     alignPanel.validateAnnotationDimensions(true);
5624     alignPanel.alignmentChanged();
5625   }
5626
5627   /**
5628    * Store selected annotation sort order for the view and repaint.
5629    */
5630   @Override
5631   protected void sortAnnotations_actionPerformed()
5632   {
5633     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5634     this.alignPanel.av
5635             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5636     alignPanel.paintAlignment(false, false);
5637   }
5638
5639   /**
5640    *
5641    * @return alignment panels in this alignment frame
5642    */
5643   public List<? extends AlignmentViewPanel> getAlignPanels()
5644   {
5645     // alignPanels is never null
5646     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5647     return alignPanels;
5648   }
5649
5650   /**
5651    * Open a new alignment window, with the cDNA associated with this (protein)
5652    * alignment, aligned as is the protein.
5653    */
5654   protected void viewAsCdna_actionPerformed()
5655   {
5656     // TODO no longer a menu action - refactor as required
5657     final AlignmentI alignment = getViewport().getAlignment();
5658     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5659     if (mappings == null)
5660     {
5661       return;
5662     }
5663     List<SequenceI> cdnaSeqs = new ArrayList<>();
5664     for (SequenceI aaSeq : alignment.getSequences())
5665     {
5666       for (AlignedCodonFrame acf : mappings)
5667       {
5668         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5669         if (dnaSeq != null)
5670         {
5671           /*
5672            * There is a cDNA mapping for this protein sequence - add to new
5673            * alignment. It will share the same dataset sequence as other mapped
5674            * cDNA (no new mappings need to be created).
5675            */
5676           final Sequence newSeq = new Sequence(dnaSeq);
5677           newSeq.setDatasetSequence(dnaSeq);
5678           cdnaSeqs.add(newSeq);
5679         }
5680       }
5681     }
5682     if (cdnaSeqs.size() == 0)
5683     {
5684       // show a warning dialog no mapped cDNA
5685       return;
5686     }
5687     AlignmentI cdna = new Alignment(
5688             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5689     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5690             AlignFrame.DEFAULT_HEIGHT);
5691     cdna.alignAs(alignment);
5692     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5693             + this.title;
5694     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5695             AlignFrame.DEFAULT_HEIGHT);
5696   }
5697
5698   /**
5699    * Set visibility of dna/protein complement view (available when shown in a
5700    * split frame).
5701    *
5702    * @param show
5703    */
5704   @Override
5705   protected void showComplement_actionPerformed(boolean show)
5706   {
5707     SplitContainerI sf = getSplitViewContainer();
5708     if (sf != null)
5709     {
5710       sf.setComplementVisible(this, show);
5711     }
5712   }
5713
5714   /**
5715    * Generate the reverse (optionally complemented) of the selected sequences,
5716    * and add them to the alignment
5717    */
5718   @Override
5719   protected void showReverse_actionPerformed(boolean complement)
5720   {
5721     AlignmentI al = null;
5722     try
5723     {
5724       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5725       al = dna.reverseCdna(complement);
5726       viewport.addAlignment(al, "");
5727       addHistoryItem(new EditCommand(
5728               MessageManager.getString("label.add_sequences"), Action.PASTE,
5729               al.getSequencesArray(), 0, al.getWidth(),
5730               viewport.getAlignment()));
5731     } catch (Exception ex)
5732     {
5733       System.err.println(ex.getMessage());
5734       return;
5735     }
5736   }
5737
5738   /**
5739    * Try to run a script in the Groovy console, having first ensured that this
5740    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5741    * be targeted at this alignment.
5742    */
5743   @Override
5744   protected void runGroovy_actionPerformed()
5745   {
5746     Jalview.setCurrentAlignFrame(this);
5747     groovy.ui.Console console = Desktop.getGroovyConsole();
5748     if (console != null)
5749     {
5750       try
5751       {
5752         console.runScript();
5753       } catch (Exception ex)
5754       {
5755         System.err.println((ex.toString()));
5756         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5757                 MessageManager.getString("label.couldnt_run_groovy_script"),
5758                 MessageManager.getString("label.groovy_support_failed"),
5759                 JvOptionPane.ERROR_MESSAGE);
5760       }
5761     }
5762     else
5763     {
5764       System.err.println("Can't run Groovy script as console not found");
5765     }
5766   }
5767
5768   /**
5769    * Hides columns containing (or not containing) a specified feature, provided
5770    * that would not leave all columns hidden
5771    *
5772    * @param featureType
5773    * @param columnsContaining
5774    * @return
5775    */
5776   public boolean hideFeatureColumns(String featureType,
5777           boolean columnsContaining)
5778   {
5779     boolean notForHiding = avc.markColumnsContainingFeatures(
5780             columnsContaining, false, false, featureType);
5781     if (notForHiding)
5782     {
5783       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5784               false, featureType))
5785       {
5786         getViewport().hideSelectedColumns();
5787         return true;
5788       }
5789     }
5790     return false;
5791   }
5792
5793   @Override
5794   protected void selectHighlightedColumns_actionPerformed(
5795           ActionEvent actionEvent)
5796   {
5797     // include key modifier check in case user selects from menu
5798     avc.markHighlightedColumns(
5799             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5800             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5801                     | ActionEvent.CTRL_MASK)) != 0);
5802   }
5803
5804   /**
5805    * Rebuilds the Colour menu, including any user-defined colours which have
5806    * been loaded either on startup or during the session
5807    */
5808   public void buildColourMenu()
5809   {
5810     colourMenu.removeAll();
5811
5812     colourMenu.add(applyToAllGroups);
5813     colourMenu.add(textColour);
5814     colourMenu.addSeparator();
5815
5816     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5817             viewport.getAlignment(), false);
5818
5819     colourMenu.add(annotationColour);
5820     bg.add(annotationColour);
5821     colourMenu.addSeparator();
5822     colourMenu.add(conservationMenuItem);
5823     colourMenu.add(modifyConservation);
5824     colourMenu.add(abovePIDThreshold);
5825     colourMenu.add(modifyPID);
5826
5827     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5828     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5829   }
5830
5831   /**
5832    * Open a dialog (if not already open) that allows the user to select and
5833    * calculate PCA or Tree analysis
5834    */
5835   protected void openTreePcaDialog()
5836   {
5837     if (alignPanel.getCalculationDialog() == null)
5838     {
5839       new CalculationChooser(AlignFrame.this);
5840     }
5841   }
5842
5843   @Override
5844   protected void loadVcf_actionPerformed()
5845   {
5846     JalviewFileChooser chooser = new JalviewFileChooser(
5847             Cache.getProperty("LAST_DIRECTORY"));
5848     chooser.setFileView(new JalviewFileView());
5849     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5850     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5851     final AlignFrame us = this;
5852     chooser.setResponseHandler(0, new Runnable()
5853     {
5854       @Override
5855       public void run()
5856       {
5857         String choice = chooser.getSelectedFile().getPath();
5858         Cache.setProperty("LAST_DIRECTORY", choice);
5859         SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5860         new VCFLoader(choice).loadVCF(seqs, us);
5861       }
5862     });
5863     chooser.showOpenDialog(null);
5864
5865   }
5866
5867   private Rectangle lastFeatureSettingsBounds = null;
5868
5869   @Override
5870   public void setFeatureSettingsGeometry(Rectangle bounds)
5871   {
5872     lastFeatureSettingsBounds = bounds;
5873   }
5874
5875   @Override
5876   public Rectangle getFeatureSettingsGeometry()
5877   {
5878     return lastFeatureSettingsBounds;
5879   }
5880 }
5881
5882 class PrintThread extends Thread
5883 {
5884   AlignmentPanel ap;
5885
5886   public PrintThread(AlignmentPanel ap)
5887   {
5888     this.ap = ap;
5889   }
5890
5891   static PageFormat pf;
5892
5893   @Override
5894   public void run()
5895   {
5896     PrinterJob printJob = PrinterJob.getPrinterJob();
5897
5898     if (pf != null)
5899     {
5900       printJob.setPrintable(ap, pf);
5901     }
5902     else
5903     {
5904       printJob.setPrintable(ap);
5905     }
5906
5907     if (printJob.printDialog())
5908     {
5909       try
5910       {
5911         printJob.print();
5912       } catch (Exception PrintException)
5913       {
5914         PrintException.printStackTrace();
5915       }
5916     }
5917   }
5918 }