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.Locale;
  61 import java.util.Vector;
  62
  63 import javax.swing.ButtonGroup;
  64 import javax.swing.JCheckBoxMenuItem;
  65 import javax.swing.JComponent;
  66 import javax.swing.JEditorPane;
  67 import javax.swing.JInternalFrame;
  68 import javax.swing.JLabel;
  69 import javax.swing.JLayeredPane;
  70 import javax.swing.JMenu;
  71 import javax.swing.JMenuItem;
  72 import javax.swing.JPanel;
  73 import javax.swing.JScrollPane;
  74 import javax.swing.SwingUtilities;
  75
  76 import ext.vamsas.ServiceHandle;
  77 import jalview.analysis.AlignmentSorter;
  78 import jalview.analysis.AlignmentUtils;
  79 import jalview.analysis.CrossRef;
  80 import jalview.analysis.Dna;
  81 import jalview.analysis.GeneticCodeI;
  82 import jalview.analysis.ParseProperties;
  83 import jalview.analysis.SequenceIdMatcher;
  84 import jalview.api.AlignExportSettingsI;
  85 import jalview.api.AlignViewControllerGuiI;
  86 import jalview.api.AlignViewControllerI;
  87 import jalview.api.AlignViewportI;
  88 import jalview.api.AlignmentViewPanel;
  89 import jalview.api.FeatureSettingsControllerI;
  90 import jalview.api.FeatureSettingsModelI;
  91 import jalview.api.SplitContainerI;
  92 import jalview.api.ViewStyleI;
  93 import jalview.api.analysis.SimilarityParamsI;
  94 import jalview.bin.Cache;
  95 import jalview.bin.Console;
  96 import jalview.bin.Jalview;
  97 import jalview.commands.CommandI;
  98 import jalview.commands.EditCommand;
  99 import jalview.commands.EditCommand.Action;
 100 import jalview.commands.OrderCommand;
 101 import jalview.commands.RemoveGapColCommand;
 102 import jalview.commands.RemoveGapsCommand;
 103 import jalview.commands.SlideSequencesCommand;
 104 import jalview.commands.TrimRegionCommand;
 105 import jalview.datamodel.AlignExportSettingsAdapter;
 106 import jalview.datamodel.AlignedCodonFrame;
 107 import jalview.datamodel.Alignment;
 108 import jalview.datamodel.AlignmentAnnotation;
 109 import jalview.datamodel.AlignmentExportData;
 110 import jalview.datamodel.AlignmentI;
 111 import jalview.datamodel.AlignmentOrder;
 112 import jalview.datamodel.AlignmentView;
 113 import jalview.datamodel.ColumnSelection;
 114 import jalview.datamodel.HiddenColumns;
 115 import jalview.datamodel.PDBEntry;
 116 import jalview.datamodel.SeqCigar;
 117 import jalview.datamodel.Sequence;
 118 import jalview.datamodel.SequenceGroup;
 119 import jalview.datamodel.SequenceI;
 120 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 121 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 122 import jalview.io.AlignmentProperties;
 123 import jalview.io.AnnotationFile;
 124 import jalview.io.BackupFiles;
 125 import jalview.io.BioJsHTMLOutput;
 126 import jalview.io.DataSourceType;
 127 import jalview.io.FileFormat;
 128 import jalview.io.FileFormatI;
 129 import jalview.io.FileFormats;
 130 import jalview.io.FileLoader;
 131 import jalview.io.FileParse;
 132 import jalview.io.FormatAdapter;
 133 import jalview.io.HtmlSvgOutput;
 134 import jalview.io.IdentifyFile;
 135 import jalview.io.JPredFile;
 136 import jalview.io.JalviewFileChooser;
 137 import jalview.io.JalviewFileView;
 138 import jalview.io.JnetAnnotationMaker;
 139 import jalview.io.NewickFile;
 140 import jalview.io.ScoreMatrixFile;
 141 import jalview.io.TCoffeeScoreFile;
 142 import jalview.io.vcf.VCFLoader;
 143 import jalview.jbgui.GAlignFrame;
 144 import jalview.project.Jalview2XML;
 145 import jalview.schemes.ColourSchemeI;
 146 import jalview.schemes.ColourSchemes;
 147 import jalview.schemes.ResidueColourScheme;
 148 import jalview.schemes.TCoffeeColourScheme;
 149 import jalview.util.HttpUtils;
 150 import jalview.util.ImageMaker.TYPE;
 151 import jalview.util.MessageManager;
 152 import jalview.util.Platform;
 153 import jalview.viewmodel.AlignmentViewport;
 154 import jalview.viewmodel.ViewportRanges;
 155 import jalview.ws.DBRefFetcher;
 156 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 157 import jalview.ws.jws1.Discoverer;
 158 import jalview.ws.jws2.Jws2Discoverer;
 159 import jalview.ws.jws2.jabaws2.Jws2Instance;
 160 import jalview.ws.seqfetcher.DbSourceProxy;
 161
 162 /**
 163  * DOCUMENT ME!
 164  *
 165  * @author $author$
 166  * @version $Revision$
 167  */
 168 @SuppressWarnings("serial")
 169 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 170         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 171 {
 172
 173   public static final int DEFAULT_WIDTH = 700;
 174
 175   public static final int DEFAULT_HEIGHT = 500;
 176
 177   /*
 178    * The currently displayed panel (selected tabbed view if more than one)
 179    */
 180   public AlignmentPanel alignPanel;
 181
 182   AlignViewport viewport;
 183
 184   public AlignViewControllerI avc;
 185
 186   List<AlignmentPanel> alignPanels = new ArrayList<>();
 187
 188   /**
 189    * Last format used to load or save alignments in this window
 190    */
 191   FileFormatI currentFileFormat = null;
 192
 193   /**
 194    * Current filename for this alignment
 195    */
 196   String fileName = null;
 197
 198   File fileObject;
 199
 200   /**
 201    * Creates a new AlignFrame object with specific width and height.
 202    *
 203    * @param al
 204    * @param width
 205    * @param height
 206    */
 207   public AlignFrame(AlignmentI al, int width, int height)
 208   {
 209     this(al, null, width, height);
 210   }
 211
 212   /**
 213    * Creates a new AlignFrame object with specific width, height and
 214    * sequenceSetId
 215    *
 216    * @param al
 217    * @param width
 218    * @param height
 219    * @param sequenceSetId
 220    */
 221   public AlignFrame(AlignmentI al, int width, int height,
 222           String sequenceSetId)
 223   {
 224     this(al, null, width, height, sequenceSetId);
 225   }
 226
 227   /**
 228    * Creates a new AlignFrame object with specific width, height and
 229    * sequenceSetId
 230    *
 231    * @param al
 232    * @param width
 233    * @param height
 234    * @param sequenceSetId
 235    * @param viewId
 236    */
 237   public AlignFrame(AlignmentI al, int width, int height,
 238           String sequenceSetId, String viewId)
 239   {
 240     this(al, null, width, height, sequenceSetId, viewId);
 241   }
 242
 243   /**
 244    * new alignment window with hidden columns
 245    *
 246    * @param al
 247    *          AlignmentI
 248    * @param hiddenColumns
 249    *          ColumnSelection or null
 250    * @param width
 251    *          Width of alignment frame
 252    * @param height
 253    *          height of frame.
 254    */
 255   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 256           int height)
 257   {
 258     this(al, hiddenColumns, width, height, null);
 259   }
 260
 261   /**
 262    * Create alignment frame for al with hiddenColumns, a specific width and
 263    * height, and specific sequenceId
 264    *
 265    * @param al
 266    * @param hiddenColumns
 267    * @param width
 268    * @param height
 269    * @param sequenceSetId
 270    *          (may be null)
 271    */
 272   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 273           int height, String sequenceSetId)
 274   {
 275     this(al, hiddenColumns, width, height, sequenceSetId, null);
 276   }
 277
 278   /**
 279    * Create alignment frame for al with hiddenColumns, a specific width and
 280    * height, and specific sequenceId
 281    *
 282    * @param al
 283    * @param hiddenColumns
 284    * @param width
 285    * @param height
 286    * @param sequenceSetId
 287    *          (may be null)
 288    * @param viewId
 289    *          (may be null)
 290    */
 291   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 292           int height, String sequenceSetId, String viewId)
 293   {
 294     setSize(width, height);
 295
 296     if (al.getDataset() == null)
 297     {
 298       al.setDataset(null);
 299     }
 300
 301     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 302
 303     alignPanel = new AlignmentPanel(this, viewport);
 304
 305     addAlignmentPanel(alignPanel, true);
 306     init();
 307   }
 308
 309   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 310           HiddenColumns hiddenColumns, int width, int height)
 311   {
 312     setSize(width, height);
 313
 314     if (al.getDataset() == null)
 315     {
 316       al.setDataset(null);
 317     }
 318
 319     viewport = new AlignViewport(al, hiddenColumns);
 320
 321     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 322     {
 323       viewport.hideSequence(hiddenSeqs);
 324     }
 325     alignPanel = new AlignmentPanel(this, viewport);
 326     addAlignmentPanel(alignPanel, true);
 327     init();
 328   }
 329
 330   /**
 331    * Make a new AlignFrame from existing alignmentPanels
 332    *
 333    * @param ap
 334    *          AlignmentPanel
 335    * @param av
 336    *          AlignViewport
 337    */
 338   public AlignFrame(AlignmentPanel ap)
 339   {
 340     viewport = ap.av;
 341     alignPanel = ap;
 342     addAlignmentPanel(ap, false);
 343     init();
 344   }
 345
 346   /**
 347    * initalise the alignframe from the underlying viewport data and the
 348    * configurations
 349    */
 350   void init()
 351   {
 352     // setBackground(Color.white); // BH 2019
 353
 354     if (!Jalview.isHeadlessMode())
 355     {
 356       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 357     }
 358
 359     avc = new jalview.controller.AlignViewController(this, viewport,
 360             alignPanel);
 361     if (viewport.getAlignmentConservationAnnotation() == null)
 362     {
 363       // BLOSUM62Colour.setEnabled(false);
 364       conservationMenuItem.setEnabled(false);
 365       modifyConservation.setEnabled(false);
 366       // PIDColour.setEnabled(false);
 367       // abovePIDThreshold.setEnabled(false);
 368       // modifyPID.setEnabled(false);
 369     }
 370
 371     String sortby = Cache.getDefault("SORT_ALIGNMENT", "No sort");
 372
 373     if (sortby.equals("Id"))
 374     {
 375       sortIDMenuItem_actionPerformed(null);
 376     }
 377     else if (sortby.equals("Pairwise Identity"))
 378     {
 379       sortPairwiseMenuItem_actionPerformed(null);
 380     }
 381
 382     this.alignPanel.av
 383             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 384
 385     setMenusFromViewport(viewport);
 386     buildSortByAnnotationScoresMenu();
 387     calculateTree.addActionListener(new ActionListener()
 388     {
 389
 390       @Override
 391       public void actionPerformed(ActionEvent e)
 392       {
 393         openTreePcaDialog();
 394       }
 395     });
 396     buildColourMenu();
 397
 398     if (Desktop.desktop != null)
 399     {
 400       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 401       if (!Platform.isJS())
 402       {
 403         addServiceListeners();
 404       }
 405       setGUINucleotide();
 406     }
 407
 408     if (viewport.getWrapAlignment())
 409     {
 410       wrapMenuItem_actionPerformed(null);
 411     }
 412
 413     if (Cache.getDefault("SHOW_OVERVIEW", false))
 414     {
 415       this.overviewMenuItem_actionPerformed(null);
 416     }
 417
 418     addKeyListener();
 419
 420     final List<AlignmentViewPanel> selviews = new ArrayList<>();
 421     final List<AlignmentPanel> origview = new ArrayList<>();
 422     final String menuLabel = MessageManager
 423             .getString("label.copy_format_from");
 424     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 425             new ViewSetProvider()
 426             {
 427
 428               @Override
 429               public AlignmentPanel[] getAllAlignmentPanels()
 430               {
 431                 origview.clear();
 432                 origview.add(alignPanel);
 433                 // make an array of all alignment panels except for this one
 434                 List<AlignmentPanel> aps = new ArrayList<>(
 435                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 436                 aps.remove(AlignFrame.this.alignPanel);
 437                 return aps.toArray(new AlignmentPanel[aps.size()]);
 438               }
 439             }, selviews, new ItemListener()
 440             {
 441
 442               @Override
 443               public void itemStateChanged(ItemEvent e)
 444               {
 445                 if (origview.size() > 0)
 446                 {
 447                   final AlignmentPanel ap = origview.get(0);
 448
 449                   /*
 450                    * Copy the ViewStyle of the selected panel to 'this one'.
 451                    * Don't change value of 'scaleProteinAsCdna' unless copying
 452                    * from a SplitFrame.
 453                    */
 454                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 455                           .getViewStyle();
 456                   boolean fromSplitFrame = selviews.get(0)
 457                           .getAlignViewport().getCodingComplement() != null;
 458                   if (!fromSplitFrame)
 459                   {
 460                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 461                             .getViewStyle().isScaleProteinAsCdna());
 462                   }
 463                   ap.getAlignViewport().setViewStyle(vs);
 464
 465                   /*
 466                    * Also rescale ViewStyle of SplitFrame complement if there is
 467                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 468                    * the whole ViewStyle (allow cDNA protein to have different
 469                    * fonts)
 470                    */
 471                   AlignViewportI complement = ap.getAlignViewport()
 472                           .getCodingComplement();
 473                   if (complement != null && vs.isScaleProteinAsCdna())
 474                   {
 475                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 476                     ((SplitFrame) af.getSplitViewContainer())
 477                             .adjustLayout();
 478                     af.setMenusForViewport();
 479                   }
 480
 481                   ap.updateLayout();
 482                   ap.setSelected(true);
 483                   ap.alignFrame.setMenusForViewport();
 484
 485                 }
 486               }
 487             });
 488     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
 489             .indexOf("devel") > -1
 490             || Cache.getDefault("VERSION", "DEVELOPMENT")
 491                     .toLowerCase(Locale.ROOT).indexOf("test") > -1)
 492     {
 493       formatMenu.add(vsel);
 494     }
 495     addFocusListener(new FocusAdapter()
 496     {
 497       @Override
 498       public void focusGained(FocusEvent e)
 499       {
 500         Jalview.setCurrentAlignFrame(AlignFrame.this);
 501       }
 502     });
 503
 504   }
 505
 506   /**
 507    * Change the filename and format for the alignment, and enable the 'reload'
 508    * button functionality.
 509    *
 510    * @param file
 511    *          valid filename
 512    * @param format
 513    *          format of file
 514    */
 515   public void setFileName(String file, FileFormatI format)
 516   {
 517     fileName = file;
 518     setFileFormat(format);
 519     reload.setEnabled(true);
 520   }
 521
 522   /**
 523    * JavaScript will have this, maybe others. More dependable than a file name
 524    * and maintains a reference to the actual bytes loaded.
 525    *
 526    * @param file
 527    */
 528   public void setFileObject(File file)
 529   {
 530     this.fileObject = file;
 531   }
 532
 533   /**
 534    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 535    * events
 536    */
 537   void addKeyListener()
 538   {
 539     addKeyListener(new KeyAdapter()
 540     {
 541       @Override
 542       public void keyPressed(KeyEvent evt)
 543       {
 544         if (viewport.cursorMode
 545                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 546                         && evt.getKeyCode() <= KeyEvent.VK_9)
 547                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 548                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 549                 && Character.isDigit(evt.getKeyChar()))
 550         {
 551           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 552         }
 553
 554         switch (evt.getKeyCode())
 555         {
 556
 557         case 27: // escape key
 558           deselectAllSequenceMenuItem_actionPerformed(null);
 559
 560           break;
 561
 562         case KeyEvent.VK_DOWN:
 563           if (evt.isAltDown() || !viewport.cursorMode)
 564           {
 565             moveSelectedSequences(false);
 566           }
 567           if (viewport.cursorMode)
 568           {
 569             alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown());
 570           }
 571           break;
 572
 573         case KeyEvent.VK_UP:
 574           if (evt.isAltDown() || !viewport.cursorMode)
 575           {
 576             moveSelectedSequences(true);
 577           }
 578           if (viewport.cursorMode)
 579           {
 580             alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown());
 581           }
 582
 583           break;
 584
 585         case KeyEvent.VK_LEFT:
 586           if (evt.isAltDown() || !viewport.cursorMode)
 587           {
 588             slideSequences(false,
 589                     alignPanel.getSeqPanel().getKeyboardNo1());
 590           }
 591           else
 592           {
 593             alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
 594           }
 595
 596           break;
 597
 598         case KeyEvent.VK_RIGHT:
 599           if (evt.isAltDown() || !viewport.cursorMode)
 600           {
 601             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 602           }
 603           else
 604           {
 605             alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
 606           }
 607           break;
 608
 609         case KeyEvent.VK_SPACE:
 610           if (viewport.cursorMode)
 611           {
 612             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 613                     || evt.isShiftDown() || evt.isAltDown());
 614           }
 615           break;
 616
 617         // case KeyEvent.VK_A:
 618         // if (viewport.cursorMode)
 619         // {
 620         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 621         // //System.out.println("A");
 622         // }
 623         // break;
 624         /*
 625          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 626          * System.out.println("closing bracket"); } break;
 627          */
 628         case KeyEvent.VK_DELETE:
 629         case KeyEvent.VK_BACK_SPACE:
 630           if (!viewport.cursorMode)
 631           {
 632             cut_actionPerformed();
 633           }
 634           else
 635           {
 636             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 637                     || evt.isShiftDown() || evt.isAltDown());
 638           }
 639
 640           break;
 641
 642         case KeyEvent.VK_S:
 643           if (viewport.cursorMode)
 644           {
 645             alignPanel.getSeqPanel().setCursorRow();
 646           }
 647           break;
 648         case KeyEvent.VK_C:
 649           if (viewport.cursorMode && !evt.isControlDown())
 650           {
 651             alignPanel.getSeqPanel().setCursorColumn();
 652           }
 653           break;
 654         case KeyEvent.VK_P:
 655           if (viewport.cursorMode)
 656           {
 657             alignPanel.getSeqPanel().setCursorPosition();
 658           }
 659           break;
 660
 661         case KeyEvent.VK_ENTER:
 662         case KeyEvent.VK_COMMA:
 663           if (viewport.cursorMode)
 664           {
 665             alignPanel.getSeqPanel().setCursorRowAndColumn();
 666           }
 667           break;
 668
 669         case KeyEvent.VK_Q:
 670           if (viewport.cursorMode)
 671           {
 672             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 673           }
 674           break;
 675         case KeyEvent.VK_M:
 676           if (viewport.cursorMode)
 677           {
 678             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 679           }
 680           break;
 681
 682         case KeyEvent.VK_F2:
 683           viewport.cursorMode = !viewport.cursorMode;
 684           setStatus(MessageManager
 685                   .formatMessage("label.keyboard_editing_mode", new String[]
 686                   { (viewport.cursorMode ? "on" : "off") }));
 687           if (viewport.cursorMode)
 688           {
 689             ViewportRanges ranges = viewport.getRanges();
 690             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 691                     .getStartRes();
 692             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 693                     .getStartSeq();
 694           }
 695           alignPanel.getSeqPanel().seqCanvas.repaint();
 696           break;
 697
 698         case KeyEvent.VK_F1:
 699           try
 700           {
 701             Help.showHelpWindow();
 702           } catch (Exception ex)
 703           {
 704             ex.printStackTrace();
 705           }
 706           break;
 707         case KeyEvent.VK_H:
 708         {
 709           boolean toggleSeqs = !evt.isControlDown();
 710           boolean toggleCols = !evt.isShiftDown();
 711           toggleHiddenRegions(toggleSeqs, toggleCols);
 712           break;
 713         }
 714         case KeyEvent.VK_B:
 715         {
 716           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 717           boolean modifyExisting = true; // always modify, don't clear
 718                                          // evt.isShiftDown();
 719           boolean invertHighlighted = evt.isAltDown();
 720           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 721                   toggleSel);
 722           break;
 723         }
 724         case KeyEvent.VK_PAGE_UP:
 725           viewport.getRanges().pageUp();
 726           break;
 727         case KeyEvent.VK_PAGE_DOWN:
 728           viewport.getRanges().pageDown();
 729           break;
 730         }
 731       }
 732
 733       @Override
 734       public void keyReleased(KeyEvent evt)
 735       {
 736         switch (evt.getKeyCode())
 737         {
 738         case KeyEvent.VK_LEFT:
 739           if (evt.isAltDown() || !viewport.cursorMode)
 740           {
 741             viewport.firePropertyChange("alignment", null,
 742                     viewport.getAlignment().getSequences());
 743           }
 744           break;
 745
 746         case KeyEvent.VK_RIGHT:
 747           if (evt.isAltDown() || !viewport.cursorMode)
 748           {
 749             viewport.firePropertyChange("alignment", null,
 750                     viewport.getAlignment().getSequences());
 751           }
 752           break;
 753         }
 754       }
 755     });
 756   }
 757
 758   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 759   {
 760     ap.alignFrame = this;
 761     avc = new jalview.controller.AlignViewController(this, viewport,
 762             alignPanel);
 763
 764     alignPanels.add(ap);
 765
 766     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 767
 768     int aSize = alignPanels.size();
 769
 770     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 771
 772     if (aSize == 1 && ap.av.getViewName() == null)
 773     {
 774       this.getContentPane().add(ap, BorderLayout.CENTER);
 775     }
 776     else
 777     {
 778       if (aSize == 2)
 779       {
 780         setInitialTabVisible();
 781       }
 782
 783       expandViews.setEnabled(true);
 784       gatherViews.setEnabled(true);
 785       tabbedPane.addTab(ap.av.getViewName(), ap);
 786
 787       ap.setVisible(false);
 788     }
 789
 790     if (newPanel)
 791     {
 792       if (ap.av.isPadGaps())
 793       {
 794         ap.av.getAlignment().padGaps();
 795       }
 796       ap.av.updateConservation(ap);
 797       ap.av.updateConsensus(ap);
 798       ap.av.updateStrucConsensus(ap);
 799     }
 800   }
 801
 802   public void setInitialTabVisible()
 803   {
 804     expandViews.setEnabled(true);
 805     gatherViews.setEnabled(true);
 806     tabbedPane.setVisible(true);
 807     AlignmentPanel first = alignPanels.get(0);
 808     tabbedPane.addTab(first.av.getViewName(), first);
 809     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 810   }
 811
 812   public AlignViewport getViewport()
 813   {
 814     return viewport;
 815   }
 816
 817   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 818   private void addServiceListeners()
 819   {
 820     final java.beans.PropertyChangeListener thisListener;
 821     Desktop.instance.addJalviewPropertyChangeListener("services",
 822             thisListener = new java.beans.PropertyChangeListener()
 823             {
 824               @Override
 825               public void propertyChange(PropertyChangeEvent evt)
 826               {
 827                 // // System.out.println("Discoverer property change.");
 828                 // if (evt.getPropertyName().equals("services"))
 829                 {
 830                   SwingUtilities.invokeLater(new Runnable()
 831                   {
 832
 833                     @Override
 834                     public void run()
 835                     {
 836                       System.err.println(
 837                               "Rebuild WS Menu for service change");
 838                       BuildWebServiceMenu();
 839                     }
 840
 841                   });
 842                 }
 843               }
 844             });
 845     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 846     {
 847       @Override
 848       public void internalFrameClosed(
 849               javax.swing.event.InternalFrameEvent evt)
 850       {
 851         // System.out.println("deregistering discoverer listener");
 852         Desktop.instance.removeJalviewPropertyChangeListener("services",
 853                 thisListener);
 854         closeMenuItem_actionPerformed(true);
 855       }
 856     });
 857     // Finally, build the menu once to get current service state
 858     new Thread(new Runnable()
 859     {
 860       @Override
 861       public void run()
 862       {
 863         BuildWebServiceMenu();
 864       }
 865     }).start();
 866   }
 867
 868   /**
 869    * Configure menu items that vary according to whether the alignment is
 870    * nucleotide or protein
 871    */
 872   public void setGUINucleotide()
 873   {
 874     AlignmentI al = getViewport().getAlignment();
 875     boolean nucleotide = al.isNucleotide();
 876
 877     loadVcf.setVisible(nucleotide);
 878     showTranslation.setVisible(nucleotide);
 879     showReverse.setVisible(nucleotide);
 880     showReverseComplement.setVisible(nucleotide);
 881     conservationMenuItem.setEnabled(!nucleotide);
 882     modifyConservation
 883             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 884     showGroupConservation.setEnabled(!nucleotide);
 885
 886     showComplementMenuItem
 887             .setText(nucleotide ? MessageManager.getString("label.protein")
 888                     : MessageManager.getString("label.nucleotide"));
 889   }
 890
 891   /**
 892    * set up menus for the current viewport. This may be called after any
 893    * operation that affects the data in the current view (selection changed,
 894    * etc) to update the menus to reflect the new state.
 895    */
 896   @Override
 897   public void setMenusForViewport()
 898   {
 899     setMenusFromViewport(viewport);
 900   }
 901
 902   /**
 903    * Need to call this method when tabs are selected for multiple views, or when
 904    * loading from Jalview2XML.java
 905    *
 906    * @param av
 907    *          AlignViewport
 908    */
 909   public void setMenusFromViewport(AlignViewport av)
 910   {
 911     padGapsMenuitem.setSelected(av.isPadGaps());
 912     colourTextMenuItem.setSelected(av.isShowColourText());
 913     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 914     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 915     conservationMenuItem.setSelected(av.getConservationSelected());
 916     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 917     seqLimits.setSelected(av.getShowJVSuffix());
 918     idRightAlign.setSelected(av.isRightAlignIds());
 919     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 920     renderGapsMenuItem.setSelected(av.isRenderGaps());
 921     wrapMenuItem.setSelected(av.getWrapAlignment());
 922     scaleAbove.setVisible(av.getWrapAlignment());
 923     scaleLeft.setVisible(av.getWrapAlignment());
 924     scaleRight.setVisible(av.getWrapAlignment());
 925     annotationPanelMenuItem.setState(av.isShowAnnotation());
 926     /*
 927      * Show/hide annotations only enabled if annotation panel is shown
 928      */
 929     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 930     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 931     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 932     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 933     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 934     viewTextMenuItem.setSelected(av.getShowText());
 935     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 936     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 937     showGroupConservation.setSelected(av.isShowGroupConservation());
 938     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 939     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 940     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 941
 942     ColourMenuHelper.setColourSelected(colourMenu,
 943             av.getGlobalColourScheme());
 944
 945     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 946     hiddenMarkers.setState(av.getShowHiddenMarkers());
 947     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 948     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 949     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 950     autoCalculate.setSelected(av.autoCalculateConsensus);
 951     sortByTree.setSelected(av.sortByTree);
 952     listenToViewSelections.setSelected(av.followSelection);
 953
 954     showProducts.setEnabled(canShowProducts());
 955     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 956
 957     updateEditMenuBar();
 958   }
 959
 960   /**
 961    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 962    *
 963    * @param b
 964    */
 965   public void setGroovyEnabled(boolean b)
 966   {
 967     runGroovy.setEnabled(b);
 968   }
 969
 970   private IProgressIndicator progressBar;
 971
 972   /*
 973    * (non-Javadoc)
 974    *
 975    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 976    */
 977   @Override
 978   public void setProgressBar(String message, long id)
 979   {
 980     progressBar.setProgressBar(message, id);
 981   }
 982
 983   @Override
 984   public void registerHandler(final long id,
 985           final IProgressIndicatorHandler handler)
 986   {
 987     progressBar.registerHandler(id, handler);
 988   }
 989
 990   /**
 991    *
 992    * @return true if any progress bars are still active
 993    */
 994   @Override
 995   public boolean operationInProgress()
 996   {
 997     return progressBar.operationInProgress();
 998   }
 999
1000   /**
1001    * Sets the text of the status bar. Note that setting a null or empty value
1002    * will cause the status bar to be hidden, with possibly undesirable flicker
1003    * of the screen layout.
1004    */
1005   @Override
1006   public void setStatus(String text)
1007   {
1008     statusBar.setText(text == null || text.isEmpty() ? " " : text);
1009   }
1010
1011   /*
1012    * Added so Castor Mapping file can obtain Jalview Version
1013    */
1014   public String getVersion()
1015   {
1016     return Cache.getProperty("VERSION");
1017   }
1018
1019   public FeatureRenderer getFeatureRenderer()
1020   {
1021     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1022   }
1023
1024   @Override
1025   public void fetchSequence_actionPerformed()
1026   {
1027     new SequenceFetcher(this);
1028   }
1029
1030   @Override
1031   public void addFromFile_actionPerformed(ActionEvent e)
1032   {
1033     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1034   }
1035
1036   @Override
1037   public void reload_actionPerformed(ActionEvent e)
1038   {
1039     if (fileName != null)
1040     {
1041       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1042       // originating file's format
1043       // TODO: work out how to recover feature settings for correct view(s) when
1044       // file is reloaded.
1045       if (FileFormat.Jalview.equals(currentFileFormat))
1046       {
1047         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1048         for (int i = 0; i < frames.length; i++)
1049         {
1050           if (frames[i] instanceof AlignFrame && frames[i] != this
1051                   && ((AlignFrame) frames[i]).fileName != null
1052                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1053           {
1054             try
1055             {
1056               frames[i].setSelected(true);
1057               Desktop.instance.closeAssociatedWindows();
1058             } catch (java.beans.PropertyVetoException ex)
1059             {
1060             }
1061           }
1062
1063         }
1064         Desktop.instance.closeAssociatedWindows();
1065
1066         FileLoader loader = new FileLoader();
1067         DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
1068                 ? DataSourceType.URL
1069                 : DataSourceType.FILE;
1070         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1071       }
1072       else
1073       {
1074         Rectangle bounds = this.getBounds();
1075
1076         FileLoader loader = new FileLoader();
1077
1078         AlignFrame newframe = null;
1079
1080         if (fileObject == null)
1081         {
1082
1083           DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(
1084                   fileName) ? DataSourceType.URL : 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         Console.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             Console.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             Console.trace("ALIGNFRAME setting PrintWriter");
1310             PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
1311
1312             if (backupfiles != null)
1313             {
1314               Console.trace("ALIGNFRAME about to write to temp file "
1315                       + backupfiles.getTempFilePath());
1316             }
1317
1318             out.print(output);
1319             Console.trace("ALIGNFRAME about to close file");
1320             out.close();
1321             Console.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             Console.error(
1332                     "ALIGNFRAME Something happened writing the temp file");
1333             Console.error(e.getMessage());
1334             Console.debug(Cache.getStackTraceString(e));
1335           } catch (Exception ex)
1336           {
1337             lastSaveSuccessful = false;
1338             Console.error(
1339                     "ALIGNFRAME Something unexpected happened writing the temp file");
1340             Console.error(ex.getMessage());
1341             Console.debug(Cache.getStackTraceString(ex));
1342           }
1343
1344           if (doBackup)
1345           {
1346             backupfiles.setWriteSuccess(lastSaveSuccessful);
1347             Console.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             Console.trace(
1351                     "ALIGNFRAME about to rollBackupsAndRenameTempFile");
1352             lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
1353             Console.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             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         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         Console.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         Console.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, false, null);
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             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                 {
4291                   // logic for 2.11.1.4 is
4292                   // always look to see if there is a discover. if there isn't
4293                   // we can't show any Jws2 services
4294                   // if there are services available, show them - regardless of
4295                   // the 'show JWS2 preference'
4296                   // if the discoverer is running then say so
4297                   // otherwise offer to trigger discovery if 'show JWS2' is not
4298                   // enabled
4299                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4300                   if (jws2servs != null)
4301                   {
4302                     if (jws2servs.hasServices())
4303                     {
4304                       jws2servs.attachWSMenuEntry(webService, me);
4305                       for (Jws2Instance sv : jws2servs.getServices())
4306                       {
4307                         if (sv.description.toLowerCase(Locale.ROOT)
4308                                 .contains("jpred"))
4309                         {
4310                           for (JMenuItem jmi : legacyItems)
4311                           {
4312                             jmi.setVisible(false);
4313                           }
4314                         }
4315                       }
4316                     }
4317
4318                     if (jws2servs.isRunning())
4319                     {
4320                       JMenuItem tm = new JMenuItem(
4321                               "Still discovering JABA Services");
4322                       tm.setEnabled(false);
4323                       webService.add(tm);
4324                     }
4325                     else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true))
4326                     {
4327                       JMenuItem enableJws2 = new JMenuItem(
4328                               "Discover Web Services");
4329                       enableJws2.setToolTipText(
4330                               "Select to start JABA Web Service discovery (or enable option in Web Service preferences)");
4331                       enableJws2.setEnabled(true);
4332                       enableJws2.addActionListener(new ActionListener()
4333                       {
4334
4335                         @Override
4336                         public void actionPerformed(ActionEvent e)
4337                         {
4338                           // start service discoverer, but ignore preference
4339                           Desktop.instance.startServiceDiscovery(false,
4340                                   true);
4341                         }
4342                       });
4343                       webService.add(enableJws2);
4344                     }
4345                   }
4346                 }
4347                 build_urlServiceMenu(me.webService);
4348                 build_fetchdbmenu(webService);
4349                 for (JMenu item : wsmenu)
4350                 {
4351                   if (item.getItemCount() == 0)
4352                   {
4353                     item.setEnabled(false);
4354                   }
4355                   else
4356                   {
4357                     item.setEnabled(true);
4358                   }
4359                 }
4360               } catch (Exception e)
4361               {
4362                 Console.debug(
4363                         "Exception during web service menu building process.",
4364                         e);
4365               }
4366             }
4367           });
4368         } catch (Exception e)
4369         {
4370         }
4371         buildingMenu = false;
4372       }
4373     }).start();
4374
4375   }
4376
4377   /**
4378    * construct any groupURL type service menu entries.
4379    *
4380    * @param webService
4381    */
4382   protected void build_urlServiceMenu(JMenu webService)
4383   {
4384     // TODO: remove this code when 2.7 is released
4385     // DEBUG - alignmentView
4386     /*
4387      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4388      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4389      *
4390      * @Override public void actionPerformed(ActionEvent e) {
4391      * jalview.datamodel.AlignmentView
4392      * .testSelectionViews(af.viewport.getAlignment(),
4393      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4394      *
4395      * }); webService.add(testAlView);
4396      */
4397     // TODO: refactor to RestClient discoverer and merge menu entries for
4398     // rest-style services with other types of analysis/calculation service
4399     // SHmmr test client - still being implemented.
4400     // DEBUG - alignmentView
4401
4402     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4403             .getRestClients())
4404     {
4405       client.attachWSMenuEntry(
4406               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4407               this);
4408     }
4409   }
4410
4411   /**
4412    * Searches the alignment sequences for xRefs and builds the Show
4413    * Cross-References menu (formerly called Show Products), with database
4414    * sources for which cross-references are found (protein sources for a
4415    * nucleotide alignment and vice versa)
4416    *
4417    * @return true if Show Cross-references menu should be enabled
4418    */
4419   public boolean canShowProducts()
4420   {
4421     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4422     AlignmentI dataset = viewport.getAlignment().getDataset();
4423
4424     showProducts.removeAll();
4425     final boolean dna = viewport.getAlignment().isNucleotide();
4426
4427     if (seqs == null || seqs.length == 0)
4428     {
4429       // nothing to see here.
4430       return false;
4431     }
4432
4433     boolean showp = false;
4434     try
4435     {
4436       List<String> ptypes = new CrossRef(seqs, dataset)
4437               .findXrefSourcesForSequences(dna);
4438
4439       for (final String source : ptypes)
4440       {
4441         showp = true;
4442         final AlignFrame af = this;
4443         JMenuItem xtype = new JMenuItem(source);
4444         xtype.addActionListener(new ActionListener()
4445         {
4446           @Override
4447           public void actionPerformed(ActionEvent e)
4448           {
4449             showProductsFor(af.viewport.getSequenceSelection(), dna,
4450                     source);
4451           }
4452         });
4453         showProducts.add(xtype);
4454       }
4455       showProducts.setVisible(showp);
4456       showProducts.setEnabled(showp);
4457     } catch (Exception e)
4458     {
4459       Console.warn(
4460               "canShowProducts threw an exception - please report to help@jalview.org",
4461               e);
4462       return false;
4463     }
4464     return showp;
4465   }
4466
4467   /**
4468    * Finds and displays cross-references for the selected sequences (protein
4469    * products for nucleotide sequences, dna coding sequences for peptides).
4470    *
4471    * @param sel
4472    *          the sequences to show cross-references for
4473    * @param dna
4474    *          true if from a nucleotide alignment (so showing proteins)
4475    * @param source
4476    *          the database to show cross-references for
4477    */
4478   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4479           final String source)
4480   {
4481     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4482             .start();
4483   }
4484
4485   /**
4486    * Construct and display a new frame containing the translation of this
4487    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4488    */
4489   @Override
4490   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4491   {
4492     AlignmentI al = null;
4493     try
4494     {
4495       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4496
4497       al = dna.translateCdna(codeTable);
4498     } catch (Exception ex)
4499     {
4500       Console.error("Exception during translation. Please report this !",
4501               ex);
4502       final String msg = MessageManager.getString(
4503               "label.error_when_translating_sequences_submit_bug_report");
4504       final String errorTitle = MessageManager
4505               .getString("label.implementation_error")
4506               + MessageManager.getString("label.translation_failed");
4507       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4508               JvOptionPane.ERROR_MESSAGE);
4509       return;
4510     }
4511     if (al == null || al.getHeight() == 0)
4512     {
4513       final String msg = MessageManager.getString(
4514               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4515       final String errorTitle = MessageManager
4516               .getString("label.translation_failed");
4517       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4518               JvOptionPane.WARNING_MESSAGE);
4519     }
4520     else
4521     {
4522       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4523       af.setFileFormat(this.currentFileFormat);
4524       final String newTitle = MessageManager
4525               .formatMessage("label.translation_of_params", new Object[]
4526               { this.getTitle(), codeTable.getId() });
4527       af.setTitle(newTitle);
4528       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4529       {
4530         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4531         viewport.openSplitFrame(af, new Alignment(seqs));
4532       }
4533       else
4534       {
4535         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4536                 DEFAULT_HEIGHT);
4537       }
4538     }
4539   }
4540
4541   /**
4542    * Set the file format
4543    *
4544    * @param format
4545    */
4546   public void setFileFormat(FileFormatI format)
4547   {
4548     this.currentFileFormat = format;
4549   }
4550
4551   /**
4552    * Try to load a features file onto the alignment.
4553    *
4554    * @param file
4555    *          contents or path to retrieve file or a File object
4556    * @param sourceType
4557    *          access mode of file (see jalview.io.AlignFile)
4558    * @return true if features file was parsed correctly.
4559    */
4560   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4561   {
4562     // BH 2018
4563     return avc.parseFeaturesFile(file, sourceType,
4564             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4565
4566   }
4567
4568   @Override
4569   public void refreshFeatureUI(boolean enableIfNecessary)
4570   {
4571     // note - currently this is only still here rather than in the controller
4572     // because of the featureSettings hard reference that is yet to be
4573     // abstracted
4574     if (enableIfNecessary)
4575     {
4576       viewport.setShowSequenceFeatures(true);
4577       showSeqFeatures.setSelected(true);
4578     }
4579
4580   }
4581
4582   @Override
4583   public void dragEnter(DropTargetDragEvent evt)
4584   {
4585   }
4586
4587   @Override
4588   public void dragExit(DropTargetEvent evt)
4589   {
4590   }
4591
4592   @Override
4593   public void dragOver(DropTargetDragEvent evt)
4594   {
4595   }
4596
4597   @Override
4598   public void dropActionChanged(DropTargetDragEvent evt)
4599   {
4600   }
4601
4602   @Override
4603   public void drop(DropTargetDropEvent evt)
4604   {
4605     // JAL-1552 - acceptDrop required before getTransferable call for
4606     // Java's Transferable for native dnd
4607     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4608     Transferable t = evt.getTransferable();
4609
4610     final AlignFrame thisaf = this;
4611     final List<Object> files = new ArrayList<>();
4612     List<DataSourceType> protocols = new ArrayList<>();
4613
4614     try
4615     {
4616       Desktop.transferFromDropTarget(files, protocols, evt, t);
4617     } catch (Exception e)
4618     {
4619       e.printStackTrace();
4620     }
4621     if (files != null)
4622     {
4623       new Thread(new Runnable()
4624       {
4625         @Override
4626         public void run()
4627         {
4628           try
4629           {
4630             // check to see if any of these files have names matching sequences
4631             // in
4632             // the alignment
4633             SequenceIdMatcher idm = new SequenceIdMatcher(
4634                     viewport.getAlignment().getSequencesArray());
4635             /**
4636              * Object[] { String,SequenceI}
4637              */
4638             ArrayList<Object[]> filesmatched = new ArrayList<>();
4639             ArrayList<Object> filesnotmatched = new ArrayList<>();
4640             for (int i = 0; i < files.size(); i++)
4641             {
4642               // BH 2018
4643               Object file = files.get(i);
4644               String fileName = file.toString();
4645               String pdbfn = "";
4646               DataSourceType protocol = (file instanceof File
4647                       ? DataSourceType.FILE
4648                       : FormatAdapter.checkProtocol(fileName));
4649               if (protocol == DataSourceType.FILE)
4650               {
4651                 File fl;
4652                 if (file instanceof File)
4653                 {
4654                   fl = (File) file;
4655                   Platform.cacheFileData(fl);
4656                 }
4657                 else
4658                 {
4659                   fl = new File(fileName);
4660                 }
4661                 pdbfn = fl.getName();
4662               }
4663               else if (protocol == DataSourceType.URL)
4664               {
4665                 URL url = new URL(fileName);
4666                 pdbfn = url.getFile();
4667               }
4668               if (pdbfn.length() > 0)
4669               {
4670                 // attempt to find a match in the alignment
4671                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4672                 int l = 0, c = pdbfn.indexOf(".");
4673                 while (mtch == null && c != -1)
4674                 {
4675                   do
4676                   {
4677                     l = c;
4678                   } while ((c = pdbfn.indexOf(".", l)) > l);
4679                   if (l > -1)
4680                   {
4681                     pdbfn = pdbfn.substring(0, l);
4682                   }
4683                   mtch = idm.findAllIdMatches(pdbfn);
4684                 }
4685                 if (mtch != null)
4686                 {
4687                   FileFormatI type;
4688                   try
4689                   {
4690                     type = new IdentifyFile().identify(file, protocol);
4691                   } catch (Exception ex)
4692                   {
4693                     type = null;
4694                   }
4695                   if (type != null && type.isStructureFile())
4696                   {
4697                     filesmatched.add(new Object[] { file, protocol, mtch });
4698                     continue;
4699                   }
4700                 }
4701                 // File wasn't named like one of the sequences or wasn't a PDB
4702                 // file.
4703                 filesnotmatched.add(file);
4704               }
4705             }
4706             int assocfiles = 0;
4707             if (filesmatched.size() > 0)
4708             {
4709               boolean autoAssociate = Cache
4710                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4711               if (!autoAssociate)
4712               {
4713                 String msg = MessageManager.formatMessage(
4714                         "label.automatically_associate_structure_files_with_sequences_same_name",
4715                         new Object[]
4716                         { Integer.valueOf(filesmatched.size())
4717                                 .toString() });
4718                 String ttl = MessageManager.getString(
4719                         "label.automatically_associate_structure_files_by_name");
4720                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4721                         ttl, JvOptionPane.YES_NO_OPTION);
4722                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4723               }
4724               if (autoAssociate)
4725               {
4726                 for (Object[] fm : filesmatched)
4727                 {
4728                   // try and associate
4729                   // TODO: may want to set a standard ID naming formalism for
4730                   // associating PDB files which have no IDs.
4731                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4732                   {
4733                     PDBEntry pe = new AssociatePdbFileWithSeq()
4734                             .associatePdbWithSeq(fm[0].toString(),
4735                                     (DataSourceType) fm[1], toassoc, false,
4736                                     Desktop.instance);
4737                     if (pe != null)
4738                     {
4739                       System.err.println("Associated file : "
4740                               + (fm[0].toString()) + " with "
4741                               + toassoc.getDisplayId(true));
4742                       assocfiles++;
4743                     }
4744                   }
4745                   // TODO: do we need to update overview ? only if features are
4746                   // shown I guess
4747                   alignPanel.paintAlignment(true, false);
4748                 }
4749               }
4750               else
4751               {
4752                 /*
4753                  * add declined structures as sequences
4754                  */
4755                 for (Object[] o : filesmatched)
4756                 {
4757                   filesnotmatched.add(o[0]);
4758                 }
4759               }
4760             }
4761             if (filesnotmatched.size() > 0)
4762             {
4763               if (assocfiles > 0 && (Cache.getDefault(
4764                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4765                       || JvOptionPane.showConfirmDialog(thisaf,
4766                               "<html>" + MessageManager.formatMessage(
4767                                       "label.ignore_unmatched_dropped_files_info",
4768                                       new Object[]
4769                                       { Integer.valueOf(
4770                                               filesnotmatched.size())
4771                                               .toString() })
4772                                       + "</html>",
4773                               MessageManager.getString(
4774                                       "label.ignore_unmatched_dropped_files"),
4775                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4776               {
4777                 return;
4778               }
4779               for (Object fn : filesnotmatched)
4780               {
4781                 loadJalviewDataFile(fn, null, null, null);
4782               }
4783
4784             }
4785           } catch (Exception ex)
4786           {
4787             ex.printStackTrace();
4788           }
4789         }
4790       }).start();
4791     }
4792   }
4793
4794   /**
4795    * Attempt to load a "dropped" file or URL string, by testing in turn for
4796    * <ul>
4797    * <li>an Annotation file</li>
4798    * <li>a JNet file</li>
4799    * <li>a features file</li>
4800    * <li>else try to interpret as an alignment file</li>
4801    * </ul>
4802    *
4803    * @param file
4804    *          either a filename or a URL string.
4805    */
4806   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4807           FileFormatI format, SequenceI assocSeq)
4808   {
4809     // BH 2018 was String file
4810     try
4811     {
4812       if (sourceType == null)
4813       {
4814         sourceType = FormatAdapter.checkProtocol(file);
4815       }
4816       // if the file isn't identified, or not positively identified as some
4817       // other filetype (PFAM is default unidentified alignment file type) then
4818       // try to parse as annotation.
4819       boolean isAnnotation = (format == null
4820               || FileFormat.Pfam.equals(format))
4821                       ? new AnnotationFile().annotateAlignmentView(viewport,
4822                               file, sourceType)
4823                       : false;
4824
4825       if (!isAnnotation)
4826       {
4827         // first see if its a T-COFFEE score file
4828         TCoffeeScoreFile tcf = null;
4829         try
4830         {
4831           tcf = new TCoffeeScoreFile(file, sourceType);
4832           if (tcf.isValid())
4833           {
4834             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4835             {
4836               buildColourMenu();
4837               changeColour(
4838                       new TCoffeeColourScheme(viewport.getAlignment()));
4839               isAnnotation = true;
4840               setStatus(MessageManager.getString(
4841                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4842             }
4843             else
4844             {
4845               // some problem - if no warning its probable that the ID matching
4846               // process didn't work
4847               JvOptionPane.showMessageDialog(Desktop.desktop,
4848                       tcf.getWarningMessage() == null
4849                               ? MessageManager.getString(
4850                                       "label.check_file_matches_sequence_ids_alignment")
4851                               : tcf.getWarningMessage(),
4852                       MessageManager.getString(
4853                               "label.problem_reading_tcoffee_score_file"),
4854                       JvOptionPane.WARNING_MESSAGE);
4855             }
4856           }
4857           else
4858           {
4859             tcf = null;
4860           }
4861         } catch (Exception x)
4862         {
4863           Console.debug(
4864                   "Exception when processing data source as T-COFFEE score file",
4865                   x);
4866           tcf = null;
4867         }
4868         if (tcf == null)
4869         {
4870           // try to see if its a JNet 'concise' style annotation file *before*
4871           // we
4872           // try to parse it as a features file
4873           if (format == null)
4874           {
4875             format = new IdentifyFile().identify(file, sourceType);
4876           }
4877           if (FileFormat.ScoreMatrix == format)
4878           {
4879             ScoreMatrixFile sm = new ScoreMatrixFile(
4880                     new FileParse(file, sourceType));
4881             sm.parse();
4882             // todo: i18n this message
4883             setStatus(MessageManager.formatMessage(
4884                     "label.successfully_loaded_matrix",
4885                     sm.getMatrixName()));
4886           }
4887           else if (FileFormat.Jnet.equals(format))
4888           {
4889             JPredFile predictions = new JPredFile(file, sourceType);
4890             new JnetAnnotationMaker();
4891             JnetAnnotationMaker.add_annotation(predictions,
4892                     viewport.getAlignment(), 0, false);
4893             viewport.getAlignment().setupJPredAlignment();
4894             isAnnotation = true;
4895           }
4896           // else if (IdentifyFile.FeaturesFile.equals(format))
4897           else if (FileFormat.Features.equals(format))
4898           {
4899             if (parseFeaturesFile(file, sourceType))
4900             {
4901               SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
4902               if (splitFrame != null)
4903               {
4904                 splitFrame.repaint();
4905               }
4906               else
4907               {
4908                 alignPanel.paintAlignment(true, true);
4909               }
4910             }
4911           }
4912           else
4913           {
4914             new FileLoader().LoadFile(viewport, file, sourceType, format);
4915           }
4916         }
4917       }
4918       if (isAnnotation)
4919       {
4920
4921         alignPanel.adjustAnnotationHeight();
4922         viewport.updateSequenceIdColours();
4923         buildSortByAnnotationScoresMenu();
4924         alignPanel.paintAlignment(true, true);
4925       }
4926     } catch (Exception ex)
4927     {
4928       ex.printStackTrace();
4929     } catch (OutOfMemoryError oom)
4930     {
4931       try
4932       {
4933         System.gc();
4934       } catch (Exception x)
4935       {
4936       }
4937       new OOMWarning(
4938               "loading data "
4939                       + (sourceType != null
4940                               ? (sourceType == DataSourceType.PASTE
4941                                       ? "from clipboard."
4942                                       : "using " + sourceType + " from "
4943                                               + file)
4944                               : ".")
4945                       + (format != null
4946                               ? "(parsing as '" + format + "' file)"
4947                               : ""),
4948               oom, Desktop.desktop);
4949     }
4950   }
4951
4952   /**
4953    * Method invoked by the ChangeListener on the tabbed pane, in other words
4954    * when a different tabbed pane is selected by the user or programmatically.
4955    */
4956   @Override
4957   public void tabSelectionChanged(int index)
4958   {
4959     if (index > -1)
4960     {
4961       alignPanel = alignPanels.get(index);
4962       viewport = alignPanel.av;
4963       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4964       setMenusFromViewport(viewport);
4965       if (featureSettings != null && featureSettings.isOpen()
4966               && featureSettings.fr.getViewport() != viewport)
4967       {
4968         if (viewport.isShowSequenceFeatures())
4969         {
4970           // refresh the featureSettings to reflect UI change
4971           showFeatureSettingsUI();
4972         }
4973         else
4974         {
4975           // close feature settings for this view.
4976           featureSettings.close();
4977         }
4978       }
4979
4980     }
4981
4982     /*
4983      * 'focus' any colour slider that is open to the selected viewport
4984      */
4985     if (viewport.getConservationSelected())
4986     {
4987       SliderPanel.setConservationSlider(alignPanel,
4988               viewport.getResidueShading(), alignPanel.getViewName());
4989     }
4990     else
4991     {
4992       SliderPanel.hideConservationSlider();
4993     }
4994     if (viewport.getAbovePIDThreshold())
4995     {
4996       SliderPanel.setPIDSliderSource(alignPanel,
4997               viewport.getResidueShading(), alignPanel.getViewName());
4998     }
4999     else
5000     {
5001       SliderPanel.hidePIDSlider();
5002     }
5003
5004     /*
5005      * If there is a frame linked to this one in a SplitPane, switch it to the
5006      * same view tab index. No infinite recursion of calls should happen, since
5007      * tabSelectionChanged() should not get invoked on setting the selected
5008      * index to an unchanged value. Guard against setting an invalid index
5009      * before the new view peer tab has been created.
5010      */
5011     final AlignViewportI peer = viewport.getCodingComplement();
5012     if (peer != null)
5013     {
5014       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
5015               .getAlignPanel().alignFrame;
5016       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
5017       {
5018         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
5019       }
5020     }
5021   }
5022
5023   /**
5024    * On right mouse click on view tab, prompt for and set new view name.
5025    */
5026   @Override
5027   public void tabbedPane_mousePressed(MouseEvent e)
5028   {
5029     if (e.isPopupTrigger())
5030     {
5031       String msg = MessageManager.getString("label.enter_view_name");
5032       String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
5033       String reply = JvOptionPane.showInputDialog(msg, ttl);
5034
5035       if (reply != null)
5036       {
5037         viewport.setViewName(reply);
5038         // TODO warn if reply is in getExistingViewNames()?
5039         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
5040       }
5041     }
5042   }
5043
5044   public AlignViewport getCurrentView()
5045   {
5046     return viewport;
5047   }
5048
5049   /**
5050    * Open the dialog for regex description parsing.
5051    */
5052   @Override
5053   protected void extractScores_actionPerformed(ActionEvent e)
5054   {
5055     ParseProperties pp = new jalview.analysis.ParseProperties(
5056             viewport.getAlignment());
5057     // TODO: verify regex and introduce GUI dialog for version 2.5
5058     // if (pp.getScoresFromDescription("col", "score column ",
5059     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
5060     // true)>0)
5061     if (pp.getScoresFromDescription("description column",
5062             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
5063     {
5064       buildSortByAnnotationScoresMenu();
5065     }
5066   }
5067
5068   /*
5069    * (non-Javadoc)
5070    *
5071    * @see
5072    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
5073    * )
5074    */
5075   @Override
5076   protected void showDbRefs_actionPerformed(ActionEvent e)
5077   {
5078     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
5079   }
5080
5081   /*
5082    * (non-Javadoc)
5083    *
5084    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
5085    * ActionEvent)
5086    */
5087   @Override
5088   protected void showNpFeats_actionPerformed(ActionEvent e)
5089   {
5090     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
5091   }
5092
5093   /**
5094    * find the viewport amongst the tabs in this alignment frame and close that
5095    * tab
5096    *
5097    * @param av
5098    */
5099   public boolean closeView(AlignViewportI av)
5100   {
5101     if (viewport == av)
5102     {
5103       this.closeMenuItem_actionPerformed(false);
5104       return true;
5105     }
5106     Component[] comp = tabbedPane.getComponents();
5107     for (int i = 0; comp != null && i < comp.length; i++)
5108     {
5109       if (comp[i] instanceof AlignmentPanel)
5110       {
5111         if (((AlignmentPanel) comp[i]).av == av)
5112         {
5113           // close the view.
5114           closeView((AlignmentPanel) comp[i]);
5115           return true;
5116         }
5117       }
5118     }
5119     return false;
5120   }
5121
5122   protected void build_fetchdbmenu(JMenu webService)
5123   {
5124     // Temporary hack - DBRef Fetcher always top level ws entry.
5125     // TODO We probably want to store a sequence database checklist in
5126     // preferences and have checkboxes.. rather than individual sources selected
5127     // here
5128     final JMenu rfetch = new JMenu(
5129             MessageManager.getString("action.fetch_db_references"));
5130     rfetch.setToolTipText(MessageManager.getString(
5131             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5132     webService.add(rfetch);
5133
5134     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5135             MessageManager.getString("option.trim_retrieved_seqs"));
5136     trimrs.setToolTipText(
5137             MessageManager.getString("label.trim_retrieved_sequences"));
5138     trimrs.setSelected(
5139             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5140     trimrs.addActionListener(new ActionListener()
5141     {
5142       @Override
5143       public void actionPerformed(ActionEvent e)
5144       {
5145         trimrs.setSelected(trimrs.isSelected());
5146         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5147                 Boolean.valueOf(trimrs.isSelected()).toString());
5148       }
5149     });
5150     rfetch.add(trimrs);
5151     JMenuItem fetchr = new JMenuItem(
5152             MessageManager.getString("label.standard_databases"));
5153     fetchr.setToolTipText(
5154             MessageManager.getString("label.fetch_embl_uniprot"));
5155     fetchr.addActionListener(new ActionListener()
5156     {
5157
5158       @Override
5159       public void actionPerformed(ActionEvent e)
5160       {
5161         new Thread(new Runnable()
5162         {
5163           @Override
5164           public void run()
5165           {
5166             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5167                     .getAlignment().isNucleotide();
5168             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5169                     alignPanel.av.getSequenceSelection(),
5170                     alignPanel.alignFrame, null,
5171                     alignPanel.alignFrame.featureSettings, isNucleotide);
5172             dbRefFetcher.addListener(new FetchFinishedListenerI()
5173             {
5174               @Override
5175               public void finished()
5176               {
5177
5178                 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5179                         .getFeatureSettingsModels())
5180                 {
5181
5182                   alignPanel.av.mergeFeaturesStyle(srcSettings);
5183                 }
5184                 AlignFrame.this.setMenusForViewport();
5185               }
5186             });
5187             dbRefFetcher.fetchDBRefs(false);
5188           }
5189         }).start();
5190
5191       }
5192
5193     });
5194     rfetch.add(fetchr);
5195     new Thread(new Runnable()
5196     {
5197       @Override
5198       public void run()
5199       {
5200         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5201                 .getSequenceFetcherSingleton();
5202         javax.swing.SwingUtilities.invokeLater(new Runnable()
5203         {
5204           @Override
5205           public void run()
5206           {
5207             String[] dbclasses = sf.getNonAlignmentSources();
5208             List<DbSourceProxy> otherdb;
5209             JMenu dfetch = new JMenu();
5210             JMenu ifetch = new JMenu();
5211             JMenuItem fetchr = null;
5212             int comp = 0, icomp = 0, mcomp = 15;
5213             String mname = null;
5214             int dbi = 0;
5215             for (String dbclass : dbclasses)
5216             {
5217               otherdb = sf.getSourceProxy(dbclass);
5218               // add a single entry for this class, or submenu allowing 'fetch
5219               // all' or pick one
5220               if (otherdb == null || otherdb.size() < 1)
5221               {
5222                 continue;
5223               }
5224               if (mname == null)
5225               {
5226                 mname = "From " + dbclass;
5227               }
5228               if (otherdb.size() == 1)
5229               {
5230                 final DbSourceProxy[] dassource = otherdb
5231                         .toArray(new DbSourceProxy[0]);
5232                 DbSourceProxy src = otherdb.get(0);
5233                 fetchr = new JMenuItem(src.getDbSource());
5234                 fetchr.addActionListener(new ActionListener()
5235                 {
5236
5237                   @Override
5238                   public void actionPerformed(ActionEvent e)
5239                   {
5240                     new Thread(new Runnable()
5241                     {
5242
5243                       @Override
5244                       public void run()
5245                       {
5246                         boolean isNucleotide = alignPanel.alignFrame
5247                                 .getViewport().getAlignment()
5248                                 .isNucleotide();
5249                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5250                                 alignPanel.av.getSequenceSelection(),
5251                                 alignPanel.alignFrame, dassource,
5252                                 alignPanel.alignFrame.featureSettings,
5253                                 isNucleotide);
5254                         dbRefFetcher
5255                                 .addListener(new FetchFinishedListenerI()
5256                                 {
5257                                   @Override
5258                                   public void finished()
5259                                   {
5260                                     FeatureSettingsModelI srcSettings = dassource[0]
5261                                             .getFeatureColourScheme();
5262                                     alignPanel.av.mergeFeaturesStyle(
5263                                             srcSettings);
5264                                     AlignFrame.this.setMenusForViewport();
5265                                   }
5266                                 });
5267                         dbRefFetcher.fetchDBRefs(false);
5268                       }
5269                     }).start();
5270                   }
5271
5272                 });
5273                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5274                         MessageManager.formatMessage(
5275                                 "label.fetch_retrieve_from", new Object[]
5276                                 { src.getDbName() })));
5277                 dfetch.add(fetchr);
5278                 comp++;
5279               }
5280               else
5281               {
5282                 final DbSourceProxy[] dassource = otherdb
5283                         .toArray(new DbSourceProxy[0]);
5284                 // fetch all entry
5285                 DbSourceProxy src = otherdb.get(0);
5286                 fetchr = new JMenuItem(MessageManager
5287                         .formatMessage("label.fetch_all_param", new Object[]
5288                         { src.getDbSource() }));
5289                 fetchr.addActionListener(new ActionListener()
5290                 {
5291                   @Override
5292                   public void actionPerformed(ActionEvent e)
5293                   {
5294                     new Thread(new Runnable()
5295                     {
5296
5297                       @Override
5298                       public void run()
5299                       {
5300                         boolean isNucleotide = alignPanel.alignFrame
5301                                 .getViewport().getAlignment()
5302                                 .isNucleotide();
5303                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5304                                 alignPanel.av.getSequenceSelection(),
5305                                 alignPanel.alignFrame, dassource,
5306                                 alignPanel.alignFrame.featureSettings,
5307                                 isNucleotide);
5308                         dbRefFetcher
5309                                 .addListener(new FetchFinishedListenerI()
5310                                 {
5311                                   @Override
5312                                   public void finished()
5313                                   {
5314                                     AlignFrame.this.setMenusForViewport();
5315                                   }
5316                                 });
5317                         dbRefFetcher.fetchDBRefs(false);
5318                       }
5319                     }).start();
5320                   }
5321                 });
5322
5323                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5324                         MessageManager.formatMessage(
5325                                 "label.fetch_retrieve_from_all_sources",
5326                                 new Object[]
5327                                 { Integer.valueOf(otherdb.size())
5328                                         .toString(),
5329                                     src.getDbSource(), src.getDbName() })));
5330                 dfetch.add(fetchr);
5331                 comp++;
5332                 // and then build the rest of the individual menus
5333                 ifetch = new JMenu(MessageManager.formatMessage(
5334                         "label.source_from_db_source", new Object[]
5335                         { src.getDbSource() }));
5336                 icomp = 0;
5337                 String imname = null;
5338                 int i = 0;
5339                 for (DbSourceProxy sproxy : otherdb)
5340                 {
5341                   String dbname = sproxy.getDbName();
5342                   String sname = dbname.length() > 5
5343                           ? dbname.substring(0, 5) + "..."
5344                           : dbname;
5345                   String msname = dbname.length() > 10
5346                           ? dbname.substring(0, 10) + "..."
5347                           : dbname;
5348                   if (imname == null)
5349                   {
5350                     imname = MessageManager
5351                             .formatMessage("label.from_msname", new Object[]
5352                             { sname });
5353                   }
5354                   fetchr = new JMenuItem(msname);
5355                   final DbSourceProxy[] dassrc = { sproxy };
5356                   fetchr.addActionListener(new ActionListener()
5357                   {
5358
5359                     @Override
5360                     public void actionPerformed(ActionEvent e)
5361                     {
5362                       new Thread(new Runnable()
5363                       {
5364
5365                         @Override
5366                         public void run()
5367                         {
5368                           boolean isNucleotide = alignPanel.alignFrame
5369                                   .getViewport().getAlignment()
5370                                   .isNucleotide();
5371                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5372                                   alignPanel.av.getSequenceSelection(),
5373                                   alignPanel.alignFrame, dassrc,
5374                                   alignPanel.alignFrame.featureSettings,
5375                                   isNucleotide);
5376                           dbRefFetcher
5377                                   .addListener(new FetchFinishedListenerI()
5378                                   {
5379                                     @Override
5380                                     public void finished()
5381                                     {
5382                                       AlignFrame.this.setMenusForViewport();
5383                                     }
5384                                   });
5385                           dbRefFetcher.fetchDBRefs(false);
5386                         }
5387                       }).start();
5388                     }
5389
5390                   });
5391                   fetchr.setToolTipText(
5392                           "<html>" + MessageManager.formatMessage(
5393                                   "label.fetch_retrieve_from", new Object[]
5394                                   { dbname }));
5395                   ifetch.add(fetchr);
5396                   ++i;
5397                   if (++icomp >= mcomp || i == (otherdb.size()))
5398                   {
5399                     ifetch.setText(MessageManager.formatMessage(
5400                             "label.source_to_target", imname, sname));
5401                     dfetch.add(ifetch);
5402                     ifetch = new JMenu();
5403                     imname = null;
5404                     icomp = 0;
5405                     comp++;
5406                   }
5407                 }
5408               }
5409               ++dbi;
5410               if (comp >= mcomp || dbi >= (dbclasses.length))
5411               {
5412                 dfetch.setText(MessageManager.formatMessage(
5413                         "label.source_to_target", mname, dbclass));
5414                 rfetch.add(dfetch);
5415                 dfetch = new JMenu();
5416                 mname = null;
5417                 comp = 0;
5418               }
5419             }
5420           }
5421         });
5422       }
5423     }).start();
5424
5425   }
5426
5427   /**
5428    * Left justify the whole alignment.
5429    */
5430   @Override
5431   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5432   {
5433     avc.justify_Region(true);
5434   }
5435
5436   /**
5437    * Right justify the whole alignment.
5438    */
5439   @Override
5440   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5441   {
5442     avc.justify_Region(false);
5443   }
5444
5445   @Override
5446   public void setShowSeqFeatures(boolean b)
5447   {
5448     showSeqFeatures.setSelected(b);
5449     viewport.setShowSequenceFeatures(b);
5450   }
5451
5452   /*
5453    * (non-Javadoc)
5454    *
5455    * @see
5456    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5457    * awt.event.ActionEvent)
5458    */
5459   @Override
5460   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5461   {
5462     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5463     alignPanel.paintAlignment(false, false);
5464   }
5465
5466   /*
5467    * (non-Javadoc)
5468    *
5469    * @see
5470    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5471    * .ActionEvent)
5472    */
5473   @Override
5474   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5475   {
5476     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5477     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5478
5479   }
5480
5481   /*
5482    * (non-Javadoc)
5483    *
5484    * @see
5485    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5486    * .event.ActionEvent)
5487    */
5488   @Override
5489   protected void showGroupConservation_actionPerformed(ActionEvent e)
5490   {
5491     viewport.setShowGroupConservation(showGroupConservation.getState());
5492     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5493   }
5494
5495   /*
5496    * (non-Javadoc)
5497    *
5498    * @see
5499    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5500    * .event.ActionEvent)
5501    */
5502   @Override
5503   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5504   {
5505     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5506     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5507   }
5508
5509   /*
5510    * (non-Javadoc)
5511    *
5512    * @see
5513    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5514    * .event.ActionEvent)
5515    */
5516   @Override
5517   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5518   {
5519     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5520     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5521   }
5522
5523   @Override
5524   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5525   {
5526     showSequenceLogo.setState(true);
5527     viewport.setShowSequenceLogo(true);
5528     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5529     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5530   }
5531
5532   @Override
5533   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5534   {
5535     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5536   }
5537
5538   /*
5539    * (non-Javadoc)
5540    *
5541    * @see
5542    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5543    * .event.ActionEvent)
5544    */
5545   @Override
5546   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5547   {
5548     if (avc.makeGroupsFromSelection())
5549     {
5550       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5551       alignPanel.updateAnnotation();
5552       alignPanel.paintAlignment(true,
5553               viewport.needToUpdateStructureViews());
5554     }
5555   }
5556
5557   public void clearAlignmentSeqRep()
5558   {
5559     // TODO refactor alignmentseqrep to controller
5560     if (viewport.getAlignment().hasSeqrep())
5561     {
5562       viewport.getAlignment().setSeqrep(null);
5563       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5564       alignPanel.updateAnnotation();
5565       alignPanel.paintAlignment(true, true);
5566     }
5567   }
5568
5569   @Override
5570   protected void createGroup_actionPerformed(ActionEvent e)
5571   {
5572     if (avc.createGroup())
5573     {
5574       if (applyAutoAnnotationSettings.isSelected())
5575       {
5576         alignPanel.updateAnnotation(true, false);
5577       }
5578       alignPanel.alignmentChanged();
5579     }
5580   }
5581
5582   @Override
5583   protected void unGroup_actionPerformed(ActionEvent e)
5584   {
5585     if (avc.unGroup())
5586     {
5587       alignPanel.alignmentChanged();
5588     }
5589   }
5590
5591   /**
5592    * make the given alignmentPanel the currently selected tab
5593    *
5594    * @param alignmentPanel
5595    */
5596   public void setDisplayedView(AlignmentPanel alignmentPanel)
5597   {
5598     if (!viewport.getSequenceSetId()
5599             .equals(alignmentPanel.av.getSequenceSetId()))
5600     {
5601       throw new Error(MessageManager.getString(
5602               "error.implementation_error_cannot_show_view_alignment_frame"));
5603     }
5604     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5605             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5606     {
5607       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5608     }
5609   }
5610
5611   /**
5612    * Action on selection of menu options to Show or Hide annotations.
5613    *
5614    * @param visible
5615    * @param forSequences
5616    *          update sequence-related annotations
5617    * @param forAlignment
5618    *          update non-sequence-related annotations
5619    */
5620   @Override
5621   protected void setAnnotationsVisibility(boolean visible,
5622           boolean forSequences, boolean forAlignment)
5623   {
5624     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5625             .getAlignmentAnnotation();
5626     if (anns == null)
5627     {
5628       return;
5629     }
5630     for (AlignmentAnnotation aa : anns)
5631     {
5632       /*
5633        * don't display non-positional annotations on an alignment
5634        */
5635       if (aa.annotations == null)
5636       {
5637         continue;
5638       }
5639       boolean apply = (aa.sequenceRef == null && forAlignment)
5640               || (aa.sequenceRef != null && forSequences);
5641       if (apply)
5642       {
5643         aa.visible = visible;
5644       }
5645     }
5646     alignPanel.validateAnnotationDimensions(true);
5647     alignPanel.alignmentChanged();
5648   }
5649
5650   /**
5651    * Store selected annotation sort order for the view and repaint.
5652    */
5653   @Override
5654   protected void sortAnnotations_actionPerformed()
5655   {
5656     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5657     this.alignPanel.av
5658             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5659     alignPanel.paintAlignment(false, false);
5660   }
5661
5662   /**
5663    *
5664    * @return alignment panels in this alignment frame
5665    */
5666   public List<? extends AlignmentViewPanel> getAlignPanels()
5667   {
5668     // alignPanels is never null
5669     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5670     return alignPanels;
5671   }
5672
5673   /**
5674    * Open a new alignment window, with the cDNA associated with this (protein)
5675    * alignment, aligned as is the protein.
5676    */
5677   protected void viewAsCdna_actionPerformed()
5678   {
5679     // TODO no longer a menu action - refactor as required
5680     final AlignmentI alignment = getViewport().getAlignment();
5681     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5682     if (mappings == null)
5683     {
5684       return;
5685     }
5686     List<SequenceI> cdnaSeqs = new ArrayList<>();
5687     for (SequenceI aaSeq : alignment.getSequences())
5688     {
5689       for (AlignedCodonFrame acf : mappings)
5690       {
5691         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5692         if (dnaSeq != null)
5693         {
5694           /*
5695            * There is a cDNA mapping for this protein sequence - add to new
5696            * alignment. It will share the same dataset sequence as other mapped
5697            * cDNA (no new mappings need to be created).
5698            */
5699           final Sequence newSeq = new Sequence(dnaSeq);
5700           newSeq.setDatasetSequence(dnaSeq);
5701           cdnaSeqs.add(newSeq);
5702         }
5703       }
5704     }
5705     if (cdnaSeqs.size() == 0)
5706     {
5707       // show a warning dialog no mapped cDNA
5708       return;
5709     }
5710     AlignmentI cdna = new Alignment(
5711             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5712     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5713             AlignFrame.DEFAULT_HEIGHT);
5714     cdna.alignAs(alignment);
5715     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5716             + this.title;
5717     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5718             AlignFrame.DEFAULT_HEIGHT);
5719   }
5720
5721   /**
5722    * Set visibility of dna/protein complement view (available when shown in a
5723    * split frame).
5724    *
5725    * @param show
5726    */
5727   @Override
5728   protected void showComplement_actionPerformed(boolean show)
5729   {
5730     SplitContainerI sf = getSplitViewContainer();
5731     if (sf != null)
5732     {
5733       sf.setComplementVisible(this, show);
5734     }
5735   }
5736
5737   /**
5738    * Generate the reverse (optionally complemented) of the selected sequences,
5739    * and add them to the alignment
5740    */
5741   @Override
5742   protected void showReverse_actionPerformed(boolean complement)
5743   {
5744     AlignmentI al = null;
5745     try
5746     {
5747       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5748       al = dna.reverseCdna(complement);
5749       viewport.addAlignment(al, "");
5750       addHistoryItem(new EditCommand(
5751               MessageManager.getString("label.add_sequences"), Action.PASTE,
5752               al.getSequencesArray(), 0, al.getWidth(),
5753               viewport.getAlignment()));
5754     } catch (Exception ex)
5755     {
5756       System.err.println(ex.getMessage());
5757       return;
5758     }
5759   }
5760
5761   /**
5762    * Try to run a script in the Groovy console, having first ensured that this
5763    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5764    * be targeted at this alignment.
5765    */
5766   @Override
5767   protected void runGroovy_actionPerformed()
5768   {
5769     Jalview.setCurrentAlignFrame(this);
5770     groovy.ui.Console console = Desktop.getGroovyConsole();
5771     if (console != null)
5772     {
5773       try
5774       {
5775         console.runScript();
5776       } catch (Exception ex)
5777       {
5778         System.err.println((ex.toString()));
5779         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5780                 MessageManager.getString("label.couldnt_run_groovy_script"),
5781                 MessageManager.getString("label.groovy_support_failed"),
5782                 JvOptionPane.ERROR_MESSAGE);
5783       }
5784     }
5785     else
5786     {
5787       System.err.println("Can't run Groovy script as console not found");
5788     }
5789   }
5790
5791   /**
5792    * Hides columns containing (or not containing) a specified feature, provided
5793    * that would not leave all columns hidden
5794    *
5795    * @param featureType
5796    * @param columnsContaining
5797    * @return
5798    */
5799   public boolean hideFeatureColumns(String featureType,
5800           boolean columnsContaining)
5801   {
5802     boolean notForHiding = avc.markColumnsContainingFeatures(
5803             columnsContaining, false, false, featureType);
5804     if (notForHiding)
5805     {
5806       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5807               false, featureType))
5808       {
5809         getViewport().hideSelectedColumns();
5810         return true;
5811       }
5812     }
5813     return false;
5814   }
5815
5816   @Override
5817   protected void selectHighlightedColumns_actionPerformed(
5818           ActionEvent actionEvent)
5819   {
5820     // include key modifier check in case user selects from menu
5821     avc.markHighlightedColumns(
5822             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5823             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5824                     | ActionEvent.CTRL_MASK)) != 0);
5825   }
5826
5827   /**
5828    * Rebuilds the Colour menu, including any user-defined colours which have
5829    * been loaded either on startup or during the session
5830    */
5831   public void buildColourMenu()
5832   {
5833     colourMenu.removeAll();
5834
5835     colourMenu.add(applyToAllGroups);
5836     colourMenu.add(textColour);
5837     colourMenu.addSeparator();
5838
5839     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5840             viewport.getAlignment(), false);
5841
5842     colourMenu.add(annotationColour);
5843     bg.add(annotationColour);
5844     colourMenu.addSeparator();
5845     colourMenu.add(conservationMenuItem);
5846     colourMenu.add(modifyConservation);
5847     colourMenu.add(abovePIDThreshold);
5848     colourMenu.add(modifyPID);
5849
5850     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5851     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5852   }
5853
5854   /**
5855    * Open a dialog (if not already open) that allows the user to select and
5856    * calculate PCA or Tree analysis
5857    */
5858   protected void openTreePcaDialog()
5859   {
5860     if (alignPanel.getCalculationDialog() == null)
5861     {
5862       new CalculationChooser(AlignFrame.this);
5863     }
5864   }
5865
5866   @Override
5867   protected void loadVcf_actionPerformed()
5868   {
5869     JalviewFileChooser chooser = new JalviewFileChooser(
5870             Cache.getProperty("LAST_DIRECTORY"));
5871     chooser.setFileView(new JalviewFileView());
5872     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5873     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5874     final AlignFrame us = this;
5875     chooser.setResponseHandler(0, new Runnable()
5876     {
5877       @Override
5878       public void run()
5879       {
5880         String choice = chooser.getSelectedFile().getPath();
5881         Cache.setProperty("LAST_DIRECTORY", choice);
5882         SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5883         new VCFLoader(choice).loadVCF(seqs, us);
5884       }
5885     });
5886     chooser.showOpenDialog(null);
5887
5888   }
5889
5890   private Rectangle lastFeatureSettingsBounds = null;
5891
5892   @Override
5893   public void setFeatureSettingsGeometry(Rectangle bounds)
5894   {
5895     lastFeatureSettingsBounds = bounds;
5896   }
5897
5898   @Override
5899   public Rectangle getFeatureSettingsGeometry()
5900   {
5901     return lastFeatureSettingsBounds;
5902   }
5903 }
5904
5905 class PrintThread extends Thread
5906 {
5907   AlignmentPanel ap;
5908
5909   public PrintThread(AlignmentPanel ap)
5910   {
5911     this.ap = ap;
5912   }
5913
5914   static PageFormat pf;
5915
5916   @Override
5917   public void run()
5918   {
5919     PrinterJob printJob = PrinterJob.getPrinterJob();
5920
5921     if (pf != null)
5922     {
5923       printJob.setPrintable(ap, pf);
5924     }
5925     else
5926     {
5927       printJob.setPrintable(ap);
5928     }
5929
5930     if (printJob.printDialog())
5931     {
5932       try
5933       {
5934         printJob.print();
5935       } catch (Exception PrintException)
5936       {
5937         PrintException.printStackTrace();
5938       }
5939     }
5940   }
5941 }