src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.GeneticCodeI;
  28 import jalview.analysis.ParseProperties;
  29 import jalview.analysis.SequenceIdMatcher;
  30 import jalview.api.AlignExportSettingsI;
  31 import jalview.api.AlignViewControllerGuiI;
  32 import jalview.api.AlignViewControllerI;
  33 import jalview.api.AlignViewportI;
  34 import jalview.api.AlignmentViewPanel;
  35 import jalview.api.FeatureSettingsControllerI;
  36 import jalview.api.SplitContainerI;
  37 import jalview.api.ViewStyleI;
  38 import jalview.api.analysis.SimilarityParamsI;
  39 import jalview.bin.Cache;
  40 import jalview.bin.Instance;
  41 import jalview.bin.Jalview;
  42 import jalview.commands.CommandI;
  43 import jalview.commands.EditCommand;
  44 import jalview.commands.EditCommand.Action;
  45 import jalview.commands.OrderCommand;
  46 import jalview.commands.RemoveGapColCommand;
  47 import jalview.commands.RemoveGapsCommand;
  48 import jalview.commands.SlideSequencesCommand;
  49 import jalview.commands.TrimRegionCommand;
  50 import jalview.datamodel.AlignExportSettingsAdapter;
  51 import jalview.datamodel.AlignedCodonFrame;
  52 import jalview.datamodel.Alignment;
  53 import jalview.datamodel.AlignmentAnnotation;
  54 import jalview.datamodel.AlignmentExportData;
  55 import jalview.datamodel.AlignmentI;
  56 import jalview.datamodel.AlignmentOrder;
  57 import jalview.datamodel.AlignmentView;
  58 import jalview.datamodel.ColumnSelection;
  59 import jalview.datamodel.HiddenColumns;
  60 import jalview.datamodel.PDBEntry;
  61 import jalview.datamodel.SeqCigar;
  62 import jalview.datamodel.Sequence;
  63 import jalview.datamodel.SequenceGroup;
  64 import jalview.datamodel.SequenceI;
  65 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  66 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  67 import jalview.io.AlignmentProperties;
  68 import jalview.io.AnnotationFile;
  69 import jalview.io.BackupFiles;
  70 import jalview.io.BioJsHTMLOutput;
  71 import jalview.io.DataSourceType;
  72 import jalview.io.FileFormat;
  73 import jalview.io.FileFormatI;
  74 import jalview.io.FileFormats;
  75 import jalview.io.FileLoader;
  76 import jalview.io.FileParse;
  77 import jalview.io.FormatAdapter;
  78 import jalview.io.HtmlSvgOutput;
  79 import jalview.io.IdentifyFile;
  80 import jalview.io.JPredFile;
  81 import jalview.io.JalviewFileChooser;
  82 import jalview.io.JalviewFileView;
  83 import jalview.io.JnetAnnotationMaker;
  84 import jalview.io.NewickFile;
  85 import jalview.io.ScoreMatrixFile;
  86 import jalview.io.TCoffeeScoreFile;
  87 import jalview.io.vcf.VCFLoader;
  88 import jalview.jbgui.GAlignFrame;
  89 import jalview.project.Jalview2XML;
  90 import jalview.schemes.ColourSchemeI;
  91 import jalview.schemes.ColourSchemes;
  92 import jalview.schemes.ResidueColourScheme;
  93 import jalview.schemes.TCoffeeColourScheme;
  94 import jalview.util.ImageMaker.TYPE;
  95 import jalview.util.MessageManager;
  96 import jalview.util.Platform;
  97 import jalview.viewmodel.AlignmentViewport;
  98 import jalview.viewmodel.ViewportRanges;
  99 import jalview.ws.DBRefFetcher;
 100 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 101 import jalview.ws.jws1.Discoverer;
 102 import jalview.ws.jws2.Jws2Discoverer;
 103 import jalview.ws.jws2.jabaws2.Jws2Instance;
 104 import jalview.ws.seqfetcher.DbSourceProxy;
 105
 106 import java.awt.BorderLayout;
 107 import java.awt.Color;
 108 import java.awt.Component;
 109 import java.awt.Rectangle;
 110 import java.awt.Toolkit;
 111 import java.awt.datatransfer.Clipboard;
 112 import java.awt.datatransfer.DataFlavor;
 113 import java.awt.datatransfer.StringSelection;
 114 import java.awt.datatransfer.Transferable;
 115 import java.awt.dnd.DnDConstants;
 116 import java.awt.dnd.DropTargetDragEvent;
 117 import java.awt.dnd.DropTargetDropEvent;
 118 import java.awt.dnd.DropTargetEvent;
 119 import java.awt.dnd.DropTargetListener;
 120 import java.awt.event.ActionEvent;
 121 import java.awt.event.ActionListener;
 122 import java.awt.event.FocusAdapter;
 123 import java.awt.event.FocusEvent;
 124 import java.awt.event.ItemEvent;
 125 import java.awt.event.ItemListener;
 126 import java.awt.event.KeyAdapter;
 127 import java.awt.event.KeyEvent;
 128 import java.awt.event.MouseEvent;
 129 import java.awt.print.PageFormat;
 130 import java.awt.print.PrinterJob;
 131 import java.beans.PropertyChangeEvent;
 132 import java.io.File;
 133 import java.io.FileWriter;
 134 import java.io.PrintWriter;
 135 import java.net.URL;
 136 import java.util.ArrayList;
 137 import java.util.Arrays;
 138 import java.util.Deque;
 139 import java.util.Enumeration;
 140 import java.util.Hashtable;
 141 import java.util.List;
 142 import java.util.Vector;
 143
 144 import javax.swing.ButtonGroup;
 145 import javax.swing.JCheckBoxMenuItem;
 146 import javax.swing.JComponent;
 147 import javax.swing.JEditorPane;
 148 import javax.swing.JInternalFrame;
 149 import javax.swing.JLabel;
 150 import javax.swing.JLayeredPane;
 151 import javax.swing.JMenu;
 152 import javax.swing.JMenuItem;
 153 import javax.swing.JPanel;
 154 import javax.swing.JScrollPane;
 155 import javax.swing.SwingUtilities;
 156
 157 import ext.vamsas.ServiceHandle;
 158
 159 /**
 160  * DOCUMENT ME!
 161  *
 162  * @author $author$
 163  * @version $Revision$
 164  */
 165 @SuppressWarnings("serial")
 166 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 167         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 168 {
 169
 170   public static final int DEFAULT_WIDTH = 700;
 171
 172   public static final int DEFAULT_HEIGHT = 500;
 173
 174   /*
 175    * The currently displayed panel (selected tabbed view if more than one)
 176    */
 177   public AlignmentPanel alignPanel;
 178
 179   AlignViewport viewport;
 180
 181   public AlignViewControllerI avc;
 182
 183   List<AlignmentPanel> alignPanels = new ArrayList<>();
 184
 185   /**
 186    * Last format used to load or save alignments in this window
 187    */
 188   FileFormatI currentFileFormat = null;
 189
 190   /**
 191    * Current filename for this alignment
 192    */
 193   String fileName = null;
 194
 195   File fileObject;
 196
 197   /**
 198    * Creates a new AlignFrame object with specific width and height.
 199    *
 200    * @param al
 201    * @param width
 202    * @param height
 203    */
 204   public AlignFrame(AlignmentI al, int width, int height)
 205   {
 206     this(al, null, width, height);
 207   }
 208
 209   /**
 210    * Creates a new AlignFrame object with specific width, height and
 211    * sequenceSetId
 212    *
 213    * @param al
 214    * @param width
 215    * @param height
 216    * @param sequenceSetId
 217    */
 218   public AlignFrame(AlignmentI al, int width, int height,
 219           String sequenceSetId)
 220   {
 221     this(al, null, width, height, sequenceSetId);
 222   }
 223
 224   /**
 225    * Creates a new AlignFrame object with specific width, height and
 226    * sequenceSetId
 227    *
 228    * @param al
 229    * @param width
 230    * @param height
 231    * @param sequenceSetId
 232    * @param viewId
 233    */
 234   public AlignFrame(AlignmentI al, int width, int height,
 235           String sequenceSetId, String viewId)
 236   {
 237     this(al, null, width, height, sequenceSetId, viewId);
 238   }
 239
 240   /**
 241    * new alignment window with hidden columns
 242    *
 243    * @param al
 244    *          AlignmentI
 245    * @param hiddenColumns
 246    *          ColumnSelection or null
 247    * @param width
 248    *          Width of alignment frame
 249    * @param height
 250    *          height of frame.
 251    */
 252   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 253           int height)
 254   {
 255     this(al, hiddenColumns, width, height, null);
 256   }
 257
 258   /**
 259    * Create alignment frame for al with hiddenColumns, a specific width and
 260    * height, and specific sequenceId
 261    *
 262    * @param al
 263    * @param hiddenColumns
 264    * @param width
 265    * @param height
 266    * @param sequenceSetId
 267    *          (may be null)
 268    */
 269   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 270           int height, String sequenceSetId)
 271   {
 272     this(al, hiddenColumns, width, height, sequenceSetId, null);
 273   }
 274
 275   /**
 276    * Create alignment frame for al with hiddenColumns, a specific width and
 277    * height, and specific sequenceId
 278    *
 279    * @param al
 280    * @param hiddenColumns
 281    * @param width
 282    * @param height
 283    * @param sequenceSetId
 284    *          (may be null)
 285    * @param viewId
 286    *          (may be null)
 287    */
 288   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 289           int height, String sequenceSetId, String viewId)
 290   {
 291     setSize(width, height);
 292
 293     if (al.getDataset() == null)
 294     {
 295       al.setDataset(null);
 296     }
 297
 298     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 299
 300     alignPanel = new AlignmentPanel(this, viewport);
 301
 302     addAlignmentPanel(alignPanel, true);
 303     init();
 304   }
 305
 306   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 307           HiddenColumns hiddenColumns, int width, int height)
 308   {
 309     setSize(width, height);
 310
 311     if (al.getDataset() == null)
 312     {
 313       al.setDataset(null);
 314     }
 315
 316     viewport = new AlignViewport(al, hiddenColumns);
 317
 318     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 319     {
 320       viewport.hideSequence(hiddenSeqs);
 321     }
 322     alignPanel = new AlignmentPanel(this, viewport);
 323     addAlignmentPanel(alignPanel, true);
 324     init();
 325   }
 326
 327   /**
 328    * Make a new AlignFrame from existing alignmentPanels
 329    *
 330    * @param ap
 331    *          AlignmentPanel
 332    * @param av
 333    *          AlignViewport
 334    */
 335   public AlignFrame(AlignmentPanel ap)
 336   {
 337     viewport = ap.av;
 338     alignPanel = ap;
 339     addAlignmentPanel(ap, false);
 340     init();
 341   }
 342
 343   /**
 344    * initalise the alignframe from the underlying viewport data and the
 345    * configurations
 346    */
 347   void init()
 348   {
 349 //        setBackground(Color.white); // BH 2019
 350
 351     if (!Jalview.isHeadlessMode())
 352     {
 353       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 354     }
 355
 356     avc = new jalview.controller.AlignViewController(this, viewport,
 357             alignPanel);
 358     if (viewport.getAlignmentConservationAnnotation() == null)
 359     {
 360       // BLOSUM62Colour.setEnabled(false);
 361       conservationMenuItem.setEnabled(false);
 362       modifyConservation.setEnabled(false);
 363       // PIDColour.setEnabled(false);
 364       // abovePIDThreshold.setEnabled(false);
 365       // modifyPID.setEnabled(false);
 366     }
 367
 368     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 369             "No sort");
 370
 371     if (sortby.equals("Id"))
 372     {
 373       sortIDMenuItem_actionPerformed(null);
 374     }
 375     else if (sortby.equals("Pairwise Identity"))
 376     {
 377       sortPairwiseMenuItem_actionPerformed(null);
 378     }
 379
 380     this.alignPanel.av
 381             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 382
 383     setMenusFromViewport(viewport);
 384     buildSortByAnnotationScoresMenu();
 385     calculateTree.addActionListener(new ActionListener()
 386     {
 387
 388       @Override
 389       public void actionPerformed(ActionEvent e)
 390       {
 391         openTreePcaDialog();
 392       }
 393     });
 394     buildColourMenu();
 395
 396     if (Desktop.getDesktopPane() != null)
 397     {
 398       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 399       if (!Platform.isJS())
 400       {
 401         addServiceListeners();
 402       }
 403       setGUINucleotide();
 404     }
 405
 406     if (viewport.getWrapAlignment())
 407     {
 408       wrapMenuItem_actionPerformed(null);
 409     }
 410
 411     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 412     {
 413       this.overviewMenuItem_actionPerformed(null);
 414     }
 415
 416     addKeyListener();
 417
 418     final List<AlignmentPanel> selviews = new ArrayList<>();
 419     final List<AlignmentPanel> origview = new ArrayList<>();
 420     final String menuLabel = MessageManager
 421             .getString("label.copy_format_from");
 422     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 423             new ViewSetProvider()
 424             {
 425
 426               @Override
 427               public AlignmentPanel[] getAllAlignmentPanels()
 428               {
 429                 origview.clear();
 430                 origview.add(alignPanel);
 431                 // make an array of all alignment panels except for this one
 432                 List<AlignmentPanel> aps = new ArrayList<>(
 433                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 434                 aps.remove(AlignFrame.this.alignPanel);
 435                 return aps.toArray(new AlignmentPanel[aps.size()]);
 436               }
 437             }, selviews, new ItemListener()
 438             {
 439
 440               @Override
 441               public void itemStateChanged(ItemEvent e)
 442               {
 443                 if (origview.size() > 0)
 444                 {
 445                   final AlignmentPanel ap = origview.get(0);
 446
 447                   /*
 448                    * Copy the ViewStyle of the selected panel to 'this one'.
 449                    * Don't change value of 'scaleProteinAsCdna' unless copying
 450                    * from a SplitFrame.
 451                    */
 452                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 453                           .getViewStyle();
 454                   boolean fromSplitFrame = selviews.get(0)
 455                           .getAlignViewport().getCodingComplement() != null;
 456                   if (!fromSplitFrame)
 457                   {
 458                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 459                             .getViewStyle().isScaleProteinAsCdna());
 460                   }
 461                   ap.getAlignViewport().setViewStyle(vs);
 462
 463                   /*
 464                    * Also rescale ViewStyle of SplitFrame complement if there is
 465                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 466                    * the whole ViewStyle (allow cDNA protein to have different
 467                    * fonts)
 468                    */
 469                   AlignViewportI complement = ap.getAlignViewport()
 470                           .getCodingComplement();
 471                   if (complement != null && vs.isScaleProteinAsCdna())
 472                   {
 473                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 474                     ((SplitFrame) af.getSplitViewContainer())
 475                             .adjustLayout();
 476                     af.setMenusForViewport();
 477                   }
 478
 479                   ap.updateLayout();
 480                   ap.setSelected(true);
 481                   ap.alignFrame.setMenusForViewport();
 482
 483                 }
 484               }
 485             });
 486     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 487             .indexOf("devel") > -1
 488             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 489                     .indexOf("test") > -1)
 490     {
 491       formatMenu.add(vsel);
 492     }
 493     addFocusListener(new FocusAdapter()
 494     {
 495       @Override
 496       public void focusGained(FocusEvent e)
 497       {
 498         Jalview.setCurrentAlignFrame(AlignFrame.this);
 499       }
 500     });
 501
 502   }
 503
 504   /**
 505    * Change the filename and format for the alignment, and enable the 'reload'
 506    * button functionality.
 507    *
 508    * @param file
 509    *          valid filename
 510    * @param format
 511    *          format of file
 512    */
 513   public void setFileName(String file, FileFormatI format)
 514   {
 515     fileName = file;
 516     setFileFormat(format);
 517     reload.setEnabled(true);
 518   }
 519
 520   /**
 521    * JavaScript will have this, maybe others. More dependable than a file name
 522    * and maintains a reference to the actual bytes loaded.
 523    *
 524    * @param file
 525    */
 526   public void setFileObject(File file)
 527   {
 528     this.fileObject = file;
 529   }
 530
 531   /**
 532    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 533    * events
 534    */
 535   void addKeyListener()
 536   {
 537     addKeyListener(new KeyAdapter()
 538     {
 539       @Override
 540       public void keyPressed(KeyEvent evt)
 541       {
 542         if (viewport.cursorMode
 543                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 544                         && evt.getKeyCode() <= KeyEvent.VK_9)
 545                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 546                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 547                 && Character.isDigit(evt.getKeyChar()))
 548         {
 549           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 550         }
 551
 552         switch (evt.getKeyCode())
 553         {
 554
 555         case 27: // escape key
 556           deselectAllSequenceMenuItem_actionPerformed(null);
 557
 558           break;
 559
 560         case KeyEvent.VK_DOWN:
 561           if (evt.isAltDown() || !viewport.cursorMode)
 562           {
 563             moveSelectedSequences(false);
 564           }
 565           if (viewport.cursorMode)
 566           {
 567             alignPanel.getSeqPanel().moveCursor(0, 1);
 568           }
 569           break;
 570
 571         case KeyEvent.VK_UP:
 572           if (evt.isAltDown() || !viewport.cursorMode)
 573           {
 574             moveSelectedSequences(true);
 575           }
 576           if (viewport.cursorMode)
 577           {
 578             alignPanel.getSeqPanel().moveCursor(0, -1);
 579           }
 580
 581           break;
 582
 583         case KeyEvent.VK_LEFT:
 584           if (evt.isAltDown() || !viewport.cursorMode)
 585           {
 586             slideSequences(false,
 587                     alignPanel.getSeqPanel().getKeyboardNo1());
 588           }
 589           else
 590           {
 591             alignPanel.getSeqPanel().moveCursor(-1, 0);
 592           }
 593
 594           break;
 595
 596         case KeyEvent.VK_RIGHT:
 597           if (evt.isAltDown() || !viewport.cursorMode)
 598           {
 599             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 600           }
 601           else
 602           {
 603             alignPanel.getSeqPanel().moveCursor(1, 0);
 604           }
 605           break;
 606
 607         case KeyEvent.VK_SPACE:
 608           if (viewport.cursorMode)
 609           {
 610             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 611                     || evt.isShiftDown() || evt.isAltDown());
 612           }
 613           break;
 614
 615         // case KeyEvent.VK_A:
 616         // if (viewport.cursorMode)
 617         // {
 618         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 619         // //System.out.println("A");
 620         // }
 621         // break;
 622         /*
 623          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 624          * System.out.println("closing bracket"); } break;
 625          */
 626         case KeyEvent.VK_DELETE:
 627         case KeyEvent.VK_BACK_SPACE:
 628           if (!viewport.cursorMode)
 629           {
 630             cut_actionPerformed();
 631           }
 632           else
 633           {
 634             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 635                     || evt.isShiftDown() || evt.isAltDown());
 636           }
 637
 638           break;
 639
 640         case KeyEvent.VK_S:
 641           if (viewport.cursorMode)
 642           {
 643             alignPanel.getSeqPanel().setCursorRow();
 644           }
 645           break;
 646         case KeyEvent.VK_C:
 647           if (viewport.cursorMode && !evt.isControlDown())
 648           {
 649             alignPanel.getSeqPanel().setCursorColumn();
 650           }
 651           break;
 652         case KeyEvent.VK_P:
 653           if (viewport.cursorMode)
 654           {
 655             alignPanel.getSeqPanel().setCursorPosition();
 656           }
 657           break;
 658
 659         case KeyEvent.VK_ENTER:
 660         case KeyEvent.VK_COMMA:
 661           if (viewport.cursorMode)
 662           {
 663             alignPanel.getSeqPanel().setCursorRowAndColumn();
 664           }
 665           break;
 666
 667         case KeyEvent.VK_Q:
 668           if (viewport.cursorMode)
 669           {
 670             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 671           }
 672           break;
 673         case KeyEvent.VK_M:
 674           if (viewport.cursorMode)
 675           {
 676             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 677           }
 678           break;
 679
 680         case KeyEvent.VK_F2:
 681           viewport.cursorMode = !viewport.cursorMode;
 682           setStatus(MessageManager
 683                   .formatMessage("label.keyboard_editing_mode", new String[]
 684                   { (viewport.cursorMode ? "on" : "off") }));
 685           if (viewport.cursorMode)
 686           {
 687             ViewportRanges ranges = viewport.getRanges();
 688             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 689                     .getStartRes();
 690             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 691                     .getStartSeq();
 692           }
 693           alignPanel.getSeqPanel().seqCanvas.repaint();
 694           break;
 695
 696         case KeyEvent.VK_F1:
 697           try
 698           {
 699             Help.showHelpWindow();
 700           } catch (Exception ex)
 701           {
 702             ex.printStackTrace();
 703           }
 704           break;
 705         case KeyEvent.VK_H:
 706         {
 707           boolean toggleSeqs = !evt.isControlDown();
 708           boolean toggleCols = !evt.isShiftDown();
 709           toggleHiddenRegions(toggleSeqs, toggleCols);
 710           break;
 711         }
 712         case KeyEvent.VK_B:
 713         {
 714           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 715           boolean modifyExisting = true; // always modify, don't clear
 716                                          // evt.isShiftDown();
 717           boolean invertHighlighted = evt.isAltDown();
 718           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 719                   toggleSel);
 720           break;
 721         }
 722         case KeyEvent.VK_PAGE_UP:
 723           viewport.getRanges().pageUp();
 724           break;
 725         case KeyEvent.VK_PAGE_DOWN:
 726           viewport.getRanges().pageDown();
 727           break;
 728         }
 729       }
 730
 731       @Override
 732       public void keyReleased(KeyEvent evt)
 733       {
 734         switch (evt.getKeyCode())
 735         {
 736         case KeyEvent.VK_LEFT:
 737           if (evt.isAltDown() || !viewport.cursorMode)
 738           {
 739             viewport.firePropertyChange("alignment", null,
 740                     viewport.getAlignment().getSequences());
 741           }
 742           break;
 743
 744         case KeyEvent.VK_RIGHT:
 745           if (evt.isAltDown() || !viewport.cursorMode)
 746           {
 747             viewport.firePropertyChange("alignment", null,
 748                     viewport.getAlignment().getSequences());
 749           }
 750           break;
 751         }
 752       }
 753     });
 754   }
 755
 756   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 757   {
 758     ap.alignFrame = this;
 759     avc = new jalview.controller.AlignViewController(this, viewport,
 760             alignPanel);
 761
 762     alignPanels.add(ap);
 763
 764     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 765
 766     int aSize = alignPanels.size();
 767
 768     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 769
 770     if (aSize == 1 && ap.av.getViewName() == null)
 771     {
 772       this.getContentPane().add(ap, BorderLayout.CENTER);
 773     }
 774     else
 775     {
 776       if (aSize == 2)
 777       {
 778         setInitialTabVisible();
 779       }
 780
 781       expandViews.setEnabled(true);
 782       gatherViews.setEnabled(true);
 783       tabbedPane.addTab(ap.av.getViewName(), ap);
 784
 785       ap.setVisible(false);
 786     }
 787
 788     if (newPanel)
 789     {
 790       if (ap.av.isPadGaps())
 791       {
 792         ap.av.getAlignment().padGaps();
 793       }
 794       ap.av.updateConservation(ap);
 795       ap.av.updateConsensus(ap);
 796       ap.av.updateStrucConsensus(ap);
 797     }
 798   }
 799
 800   public void setInitialTabVisible()
 801   {
 802     expandViews.setEnabled(true);
 803     gatherViews.setEnabled(true);
 804     tabbedPane.setVisible(true);
 805     AlignmentPanel first = alignPanels.get(0);
 806     tabbedPane.addTab(first.av.getViewName(), first);
 807     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 808   }
 809
 810   public AlignViewport getViewport()
 811   {
 812     return viewport;
 813   }
 814
 815   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 816   private void addServiceListeners()
 817   {
 818     final java.beans.PropertyChangeListener thisListener;
 819     Instance.getDesktop().addJalviewPropertyChangeListener("services",
 820             thisListener = new java.beans.PropertyChangeListener()
 821             {
 822               @Override
 823               public void propertyChange(PropertyChangeEvent evt)
 824               {
 825                 // // System.out.println("Discoverer property change.");
 826                 // if (evt.getPropertyName().equals("services"))
 827                 {
 828                   SwingUtilities.invokeLater(new Runnable()
 829                   {
 830
 831                     @Override
 832                     public void run()
 833                     {
 834                       System.err.println(
 835                               "Rebuild WS Menu for service change");
 836                       BuildWebServiceMenu();
 837                     }
 838
 839                   });
 840                 }
 841               }
 842             });
 843     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 844     {
 845       @Override
 846       public void internalFrameClosed(
 847               javax.swing.event.InternalFrameEvent evt)
 848       {
 849         // System.out.println("deregistering discoverer listener");
 850         Instance.getDesktop().removeJalviewPropertyChangeListener("services",
 851                 thisListener);
 852         closeMenuItem_actionPerformed(true);
 853       }
 854     });
 855     // Finally, build the menu once to get current service state
 856     new Thread(new Runnable()
 857     {
 858       @Override
 859       public void run()
 860       {
 861         BuildWebServiceMenu();
 862       }
 863     }).start();
 864   }
 865
 866   /**
 867    * Configure menu items that vary according to whether the alignment is
 868    * nucleotide or protein
 869    */
 870   public void setGUINucleotide()
 871   {
 872     AlignmentI al = getViewport().getAlignment();
 873     boolean nucleotide = al.isNucleotide();
 874
 875     loadVcf.setVisible(nucleotide);
 876     showTranslation.setVisible(nucleotide);
 877     showReverse.setVisible(nucleotide);
 878     showReverseComplement.setVisible(nucleotide);
 879     conservationMenuItem.setEnabled(!nucleotide);
 880     modifyConservation
 881             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 882     showGroupConservation.setEnabled(!nucleotide);
 883
 884     showComplementMenuItem
 885             .setText(nucleotide ? MessageManager.getString("label.protein")
 886                     : MessageManager.getString("label.nucleotide"));
 887   }
 888
 889   /**
 890    * set up menus for the current viewport. This may be called after any
 891    * operation that affects the data in the current view (selection changed,
 892    * etc) to update the menus to reflect the new state.
 893    */
 894   @Override
 895   public void setMenusForViewport()
 896   {
 897     setMenusFromViewport(viewport);
 898   }
 899
 900   /**
 901    * Need to call this method when tabs are selected for multiple views, or when
 902    * loading from Jalview2XML.java
 903    *
 904    * @param av
 905    *          AlignViewport
 906    */
 907   public void setMenusFromViewport(AlignViewport av)
 908   {
 909     padGapsMenuitem.setSelected(av.isPadGaps());
 910     colourTextMenuItem.setSelected(av.isShowColourText());
 911     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 912     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 913     conservationMenuItem.setSelected(av.getConservationSelected());
 914     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 915     seqLimits.setSelected(av.getShowJVSuffix());
 916     idRightAlign.setSelected(av.isRightAlignIds());
 917     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 918     renderGapsMenuItem.setSelected(av.isRenderGaps());
 919     wrapMenuItem.setSelected(av.getWrapAlignment());
 920     scaleAbove.setVisible(av.getWrapAlignment());
 921     scaleLeft.setVisible(av.getWrapAlignment());
 922     scaleRight.setVisible(av.getWrapAlignment());
 923     annotationPanelMenuItem.setState(av.isShowAnnotation());
 924     /*
 925      * Show/hide annotations only enabled if annotation panel is shown
 926      */
 927     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 928     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 929     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 930     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 931     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 932     viewTextMenuItem.setSelected(av.getShowText());
 933     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 934     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 935     showGroupConservation.setSelected(av.isShowGroupConservation());
 936     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 937     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 938     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 939
 940     ColourMenuHelper.setColourSelected(colourMenu,
 941             av.getGlobalColourScheme());
 942
 943     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 944     hiddenMarkers.setState(av.getShowHiddenMarkers());
 945     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 946     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 947     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 948     autoCalculate.setSelected(av.autoCalculateConsensus);
 949     sortByTree.setSelected(av.sortByTree);
 950     listenToViewSelections.setSelected(av.followSelection);
 951
 952     showProducts.setEnabled(canShowProducts());
 953     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 954
 955     updateEditMenuBar();
 956   }
 957
 958   /**
 959    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 960    *
 961    * @param b
 962    */
 963   public void setGroovyEnabled(boolean b)
 964   {
 965     runGroovy.setEnabled(b);
 966   }
 967
 968   private IProgressIndicator progressBar;
 969
 970   /*
 971    * (non-Javadoc)
 972    *
 973    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 974    */
 975   @Override
 976   public void setProgressBar(String message, long id)
 977   {
 978     progressBar.setProgressBar(message, id);
 979   }
 980
 981   @Override
 982   public void registerHandler(final long id,
 983           final IProgressIndicatorHandler handler)
 984   {
 985     progressBar.registerHandler(id, handler);
 986   }
 987
 988   /**
 989    *
 990    * @return true if any progress bars are still active
 991    */
 992   @Override
 993   public boolean operationInProgress()
 994   {
 995     return progressBar.operationInProgress();
 996   }
 997
 998   /**
 999    * Sets the text of the status bar. Note that setting a null or empty value
1000    * will cause the status bar to be hidden, with possibly undesirable flicker
1001    * of the screen layout.
1002    */
1003   @Override
1004   public void setStatus(String text)
1005   {
1006     statusBar.setText(text == null || text.isEmpty() ? " " : text);
1007   }
1008
1009   /*
1010    * Added so Castor Mapping file can obtain Jalview Version
1011    */
1012   public String getVersion()
1013   {
1014     return jalview.bin.Cache.getProperty("VERSION");
1015   }
1016
1017   public FeatureRenderer getFeatureRenderer()
1018   {
1019     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1020   }
1021
1022   @Override
1023   public void fetchSequence_actionPerformed()
1024   {
1025     new SequenceFetcher(this);
1026   }
1027
1028   @Override
1029   public void addFromFile_actionPerformed(ActionEvent e)
1030   {
1031     Instance.getDesktop().inputLocalFileMenuItem_actionPerformed(viewport);
1032   }
1033
1034   @Override
1035   public void reload_actionPerformed(ActionEvent e)
1036   {
1037     if (fileName != null)
1038     {
1039       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1040       // originating file's format
1041       // TODO: work out how to recover feature settings for correct view(s) when
1042       // file is reloaded.
1043       if (FileFormat.Jalview.equals(currentFileFormat))
1044       {
1045         JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
1046         for (int i = 0; i < frames.length; i++)
1047         {
1048           if (frames[i] instanceof AlignFrame && frames[i] != this
1049                   && ((AlignFrame) frames[i]).fileName != null
1050                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1051           {
1052             try
1053             {
1054               frames[i].setSelected(true);
1055               Instance.getDesktop().closeAssociatedWindows();
1056             } catch (java.beans.PropertyVetoException ex)
1057             {
1058             }
1059           }
1060
1061         }
1062         Instance.getDesktop().closeAssociatedWindows();
1063
1064         FileLoader loader = new FileLoader();
1065         DataSourceType protocol = fileName.startsWith("http:")
1066                 ? DataSourceType.URL
1067                 : DataSourceType.FILE;
1068         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1069       }
1070       else
1071       {
1072         Rectangle bounds = this.getBounds();
1073
1074         FileLoader loader = new FileLoader();
1075
1076         AlignFrame newframe = null;
1077
1078         if (fileObject == null)
1079         {
1080
1081           DataSourceType protocol = (fileName.startsWith("http:")
1082                   ? DataSourceType.URL
1083                   : DataSourceType.FILE);
1084           newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1085                   currentFileFormat);
1086         }
1087         else
1088         {
1089           newframe = loader.LoadFileWaitTillLoaded(fileObject,
1090                   DataSourceType.FILE, currentFileFormat);
1091         }
1092
1093         newframe.setBounds(bounds);
1094         if (featureSettings != null && featureSettings.isShowing())
1095         {
1096           final Rectangle fspos = featureSettings.frame.getBounds();
1097           // TODO: need a 'show feature settings' function that takes bounds -
1098           // need to refactor Desktop.addFrame
1099           newframe.featureSettings_actionPerformed(null);
1100           final FeatureSettings nfs = newframe.featureSettings;
1101           SwingUtilities.invokeLater(new Runnable()
1102           {
1103             @Override
1104             public void run()
1105             {
1106               nfs.frame.setBounds(fspos);
1107             }
1108           });
1109           this.featureSettings.close();
1110           this.featureSettings = null;
1111         }
1112         this.closeMenuItem_actionPerformed(true);
1113       }
1114     }
1115   }
1116
1117   @Override
1118   public void addFromText_actionPerformed(ActionEvent e)
1119   {
1120     Instance.getDesktop()
1121             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1122   }
1123
1124   @Override
1125   public void addFromURL_actionPerformed(ActionEvent e)
1126   {
1127     Instance.getDesktop().inputURLMenuItem_actionPerformed(viewport);
1128   }
1129
1130   @Override
1131   public void save_actionPerformed(ActionEvent e)
1132   {
1133     if (fileName == null || (currentFileFormat == null)
1134             || fileName.startsWith("http"))
1135     {
1136       saveAs_actionPerformed();
1137     }
1138     else
1139     {
1140       saveAlignment(fileName, currentFileFormat);
1141     }
1142   }
1143
1144   /**
1145    * Saves the alignment to a file with a name chosen by the user, if necessary
1146    * warning if a file would be overwritten
1147    */
1148   @Override
1149   public void saveAs_actionPerformed()
1150   {
1151     String format = currentFileFormat == null ? null
1152             : currentFileFormat.getName();
1153     JalviewFileChooser chooser = JalviewFileChooser
1154             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1155
1156     chooser.setFileView(new JalviewFileView());
1157     chooser.setDialogTitle(
1158             MessageManager.getString("label.save_alignment_to_file"));
1159     chooser.setToolTipText(MessageManager.getString("action.save"));
1160
1161     int value = chooser.showSaveDialog(this);
1162
1163     if (value != JalviewFileChooser.APPROVE_OPTION)
1164     {
1165       return;
1166     }
1167     currentFileFormat = chooser.getSelectedFormat();
1168     // todo is this (2005) test now obsolete - value is never null?
1169     while (currentFileFormat == null)
1170     {
1171       JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
1172               MessageManager
1173                       .getString("label.select_file_format_before_saving"),
1174               MessageManager.getString("label.file_format_not_specified"),
1175               JvOptionPane.WARNING_MESSAGE);
1176       currentFileFormat = chooser.getSelectedFormat();
1177       value = chooser.showSaveDialog(this);
1178       if (value != JalviewFileChooser.APPROVE_OPTION)
1179       {
1180         return;
1181       }
1182     }
1183
1184     fileName = chooser.getSelectedFile().getPath();
1185
1186     Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1187     Cache.setProperty("LAST_DIRECTORY", fileName);
1188     saveAlignment(fileName, currentFileFormat);
1189   }
1190
1191   boolean lastSaveSuccessful = false;
1192
1193   FileFormatI lastFormatSaved;
1194
1195   String lastFilenameSaved;
1196
1197   /**
1198    * Raise a dialog or status message for the last call to saveAlignment.
1199    *
1200    * @return true if last call to saveAlignment(file, format) was successful.
1201    */
1202   public boolean isSaveAlignmentSuccessful()
1203   {
1204
1205     if (!lastSaveSuccessful)
1206     {
1207       JvOptionPane.showInternalMessageDialog(this, MessageManager
1208               .formatMessage("label.couldnt_save_file", new Object[]
1209               { lastFilenameSaved }),
1210               MessageManager.getString("label.error_saving_file"),
1211               JvOptionPane.WARNING_MESSAGE);
1212     }
1213     else
1214     {
1215
1216       setStatus(MessageManager.formatMessage(
1217               "label.successfully_saved_to_file_in_format", new Object[]
1218               { lastFilenameSaved, lastFormatSaved }));
1219
1220     }
1221     return lastSaveSuccessful;
1222   }
1223
1224   /**
1225    * Saves the alignment to the specified file path, in the specified format,
1226    * which may be an alignment format, or Jalview project format. If the
1227    * alignment has hidden regions, or the format is one capable of including
1228    * non-sequence data (features, annotations, groups), then the user may be
1229    * prompted to specify what to include in the output.
1230    *
1231    * @param file
1232    * @param format
1233    */
1234   public void saveAlignment(String file, FileFormatI format)
1235   {
1236     lastSaveSuccessful = true;
1237     lastFilenameSaved = file;
1238     lastFormatSaved = format;
1239
1240     if (FileFormat.Jalview.equals(format))
1241     {
1242       String shortName = title;
1243       if (shortName.indexOf(File.separatorChar) > -1)
1244       {
1245         shortName = shortName.substring(
1246                 shortName.lastIndexOf(File.separatorChar) + 1);
1247       }
1248       lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName);
1249
1250       statusBar.setText(MessageManager.formatMessage(
1251               "label.successfully_saved_to_file_in_format", new Object[]
1252               { fileName, format }));
1253
1254       return;
1255     }
1256
1257     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1258     Runnable cancelAction = new Runnable()
1259     {
1260       @Override
1261       public void run()
1262       {
1263         lastSaveSuccessful = false;
1264       }
1265     };
1266     Runnable outputAction = new Runnable()
1267     {
1268       @Override
1269       public void run()
1270       {
1271         // todo defer this to inside formatSequences (or later)
1272         AlignmentExportData exportData = viewport
1273                 .getAlignExportData(options);
1274         String output = new FormatAdapter(alignPanel, options)
1275                 .formatSequences(format, exportData.getAlignment(),
1276                         exportData.getOmitHidden(),
1277                         exportData.getStartEndPostions(),
1278                         viewport.getAlignment().getHiddenColumns());
1279         if (output == null)
1280         {
1281           lastSaveSuccessful = false;
1282         }
1283         else
1284         {
1285           // create backupfiles object and get new temp filename destination
1286           boolean doBackup = BackupFiles.getEnabled();
1287           BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
1288           try
1289           {
1290             String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
1291                         PrintWriter out = new PrintWriter(
1292                     new FileWriter(tempFilePath));
1293
1294             out.print(output);
1295             out.close();
1296             AlignFrame.this.setTitle(file);
1297             statusBar.setText(MessageManager.formatMessage(
1298                   "label.successfully_saved_to_file_in_format", new Object[]
1299                   { fileName, format.getName() }));
1300             lastSaveSuccessful = true;
1301           } catch (Exception ex)
1302           {
1303             lastSaveSuccessful = false;
1304             ex.printStackTrace();
1305           }
1306
1307           if (doBackup)
1308           {
1309             backupfiles.setWriteSuccess(lastSaveSuccessful);
1310             // do the backup file roll and rename the temp file to actual file
1311             lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
1312           }
1313         }
1314       }
1315     };
1316
1317     /*
1318      * show dialog with export options if applicable; else just do it
1319      */
1320     if (AlignExportOptions.isNeeded(viewport, format))
1321     {
1322       AlignExportOptions choices = new AlignExportOptions(
1323               alignPanel.getAlignViewport(), format, options);
1324       choices.setResponseAction(0, outputAction);
1325       choices.setResponseAction(1, cancelAction);
1326       choices.showDialog();
1327     }
1328     else
1329     {
1330       outputAction.run();
1331     }
1332   }
1333
1334   /**
1335    * Outputs the alignment to textbox in the requested format, if necessary
1336    * first prompting the user for whether to include hidden regions or
1337    * non-sequence data
1338    *
1339    * @param fileFormatName
1340    */
1341   @Override
1342   protected void outputText_actionPerformed(String fileFormatName)
1343   {
1344     FileFormatI fileFormat = FileFormats.getInstance()
1345             .forName(fileFormatName);
1346     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1347     Runnable outputAction = new Runnable()
1348     {
1349       @Override
1350       public void run()
1351       {
1352         // todo defer this to inside formatSequences (or later)
1353         AlignmentExportData exportData = viewport
1354                 .getAlignExportData(options);
1355         CutAndPasteTransfer cap = new CutAndPasteTransfer();
1356         cap.setForInput(null);
1357         try
1358         {
1359           FileFormatI format = fileFormat;
1360           cap.setText(new FormatAdapter(alignPanel, options)
1361                   .formatSequences(format, exportData.getAlignment(),
1362                           exportData.getOmitHidden(),
1363                           exportData.getStartEndPostions(),
1364                           viewport.getAlignment().getHiddenColumns()));
1365           Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1366                   "label.alignment_output_command", new Object[]
1367                   { fileFormat.getName() }), 600, 500);
1368         } catch (OutOfMemoryError oom)
1369         {
1370           new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1371                   oom);
1372           cap.dispose();
1373         }
1374       }
1375     };
1376
1377     /*
1378      * show dialog with export options if applicable; else just do it
1379      */
1380     if (AlignExportOptions.isNeeded(viewport, fileFormat))
1381     {
1382       AlignExportOptions choices = new AlignExportOptions(
1383               alignPanel.getAlignViewport(), fileFormat, options);
1384       choices.setResponseAction(0, outputAction);
1385       choices.showDialog();
1386     }
1387     else
1388     {
1389       outputAction.run();
1390     }
1391   }
1392
1393   /**
1394    * DOCUMENT ME!
1395    *
1396    * @param e
1397    *          DOCUMENT ME!
1398    */
1399   @Override
1400   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1401   {
1402     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1403     htmlSVG.exportHTML(null);
1404   }
1405
1406   @Override
1407   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1408   {
1409     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1410     bjs.exportHTML(null);
1411   }
1412
1413   public void createImageMap(File file, String image)
1414   {
1415     alignPanel.makePNGImageMap(file, image);
1416   }
1417
1418   /**
1419    * Creates a PNG image of the alignment and writes it to the given file. If
1420    * the file is null, the user is prompted to choose a file.
1421    *
1422    * @param f
1423    */
1424   @Override
1425   public void createPNG(File f)
1426   {
1427     alignPanel.makeAlignmentImage(TYPE.PNG, f);
1428   }
1429
1430   /**
1431    * Creates an EPS image of the alignment and writes it to the given file. If
1432    * the file is null, the user is prompted to choose a file.
1433    *
1434    * @param f
1435    */
1436   @Override
1437   public void createEPS(File f)
1438   {
1439     alignPanel.makeAlignmentImage(TYPE.EPS, f);
1440   }
1441
1442   /**
1443    * Creates an SVG image of the alignment and writes it to the given file. If
1444    * the file is null, the user is prompted to choose a file.
1445    *
1446    * @param f
1447    */
1448   @Override
1449   public void createSVG(File f)
1450   {
1451     alignPanel.makeAlignmentImage(TYPE.SVG, f);
1452   }
1453
1454   @Override
1455   public void pageSetup_actionPerformed(ActionEvent e)
1456   {
1457     PrinterJob printJob = PrinterJob.getPrinterJob();
1458     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1459   }
1460
1461   /**
1462    * DOCUMENT ME!
1463    *
1464    * @param e
1465    *          DOCUMENT ME!
1466    */
1467   @Override
1468   public void printMenuItem_actionPerformed(ActionEvent e)
1469   {
1470     // Putting in a thread avoids Swing painting problems
1471     PrintThread thread = new PrintThread(alignPanel);
1472     thread.start();
1473   }
1474
1475   @Override
1476   public void exportFeatures_actionPerformed(ActionEvent e)
1477   {
1478     new AnnotationExporter(alignPanel).exportFeatures();
1479   }
1480
1481   @Override
1482   public void exportAnnotations_actionPerformed(ActionEvent e)
1483   {
1484     new AnnotationExporter(alignPanel).exportAnnotations();
1485   }
1486
1487   @Override
1488   public void associatedData_actionPerformed(ActionEvent e)
1489   {
1490     final JalviewFileChooser chooser = new JalviewFileChooser(
1491             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1492     chooser.setFileView(new JalviewFileView());
1493     chooser.setDialogTitle(
1494             MessageManager.getString("label.load_jalview_annotations"));
1495     chooser.setToolTipText(
1496             MessageManager.getString("label.load_jalview_annotations"));
1497     chooser.setResponseHandler(0, new Runnable()
1498     {
1499       @Override
1500       public void run()
1501       {
1502         String choice = chooser.getSelectedFile().getPath();
1503         jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1504         loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1505       }
1506     });
1507
1508     chooser.showOpenDialog(this);
1509   }
1510
1511   /**
1512    * Close the current view or all views in the alignment frame. If the frame
1513    * only contains one view then the alignment will be removed from memory.
1514    *
1515    * @param closeAllTabs
1516    */
1517   @Override
1518   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1519   {
1520     if (alignPanels != null && alignPanels.size() < 2)
1521     {
1522       closeAllTabs = true;
1523     }
1524
1525     try
1526     {
1527       if (alignPanels != null)
1528       {
1529         if (closeAllTabs)
1530         {
1531           if (this.isClosed())
1532           {
1533             // really close all the windows - otherwise wait till
1534             // setClosed(true) is called
1535             for (int i = 0; i < alignPanels.size(); i++)
1536             {
1537               AlignmentPanel ap = alignPanels.get(i);
1538               ap.closePanel();
1539             }
1540           }
1541         }
1542         else
1543         {
1544           closeView(alignPanel);
1545         }
1546       }
1547
1548       if (closeAllTabs)
1549       {
1550         /*
1551          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1552          * be called recursively, with the frame now in 'closed' state
1553          */
1554         this.setClosed(true);
1555       }
1556     } catch (Exception ex)
1557     {
1558       ex.printStackTrace();
1559     }
1560   }
1561
1562   /**
1563    * Close the specified panel and close up tabs appropriately.
1564    *
1565    * @param panelToClose
1566    */
1567   public void closeView(AlignmentPanel panelToClose)
1568   {
1569     int index = tabbedPane.getSelectedIndex();
1570     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1571     alignPanels.remove(panelToClose);
1572     panelToClose.closePanel();
1573     panelToClose = null;
1574
1575     tabbedPane.removeTabAt(closedindex);
1576     tabbedPane.validate();
1577
1578     if (index > closedindex || index == tabbedPane.getTabCount())
1579     {
1580       // modify currently selected tab index if necessary.
1581       index--;
1582     }
1583
1584     this.tabSelectionChanged(index);
1585   }
1586
1587   /**
1588    * DOCUMENT ME!
1589    */
1590   void updateEditMenuBar()
1591   {
1592
1593     if (viewport.getHistoryList().size() > 0)
1594     {
1595       undoMenuItem.setEnabled(true);
1596       CommandI command = viewport.getHistoryList().peek();
1597       undoMenuItem.setText(MessageManager
1598               .formatMessage("label.undo_command", new Object[]
1599               { command.getDescription() }));
1600     }
1601     else
1602     {
1603       undoMenuItem.setEnabled(false);
1604       undoMenuItem.setText(MessageManager.getString("action.undo"));
1605     }
1606
1607     if (viewport.getRedoList().size() > 0)
1608     {
1609       redoMenuItem.setEnabled(true);
1610
1611       CommandI command = viewport.getRedoList().peek();
1612       redoMenuItem.setText(MessageManager
1613               .formatMessage("label.redo_command", new Object[]
1614               { command.getDescription() }));
1615     }
1616     else
1617     {
1618       redoMenuItem.setEnabled(false);
1619       redoMenuItem.setText(MessageManager.getString("action.redo"));
1620     }
1621   }
1622
1623   @Override
1624   public void addHistoryItem(CommandI command)
1625   {
1626     if (command.getSize() > 0)
1627     {
1628       viewport.addToHistoryList(command);
1629       viewport.clearRedoList();
1630       updateEditMenuBar();
1631       viewport.updateHiddenColumns();
1632       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1633       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1634       // viewport.getColumnSelection()
1635       // .getHiddenColumns().size() > 0);
1636     }
1637   }
1638
1639   /**
1640    *
1641    * @return alignment objects for all views
1642    */
1643   AlignmentI[] getViewAlignments()
1644   {
1645     if (alignPanels != null)
1646     {
1647       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1648       int i = 0;
1649       for (AlignmentPanel ap : alignPanels)
1650       {
1651         als[i++] = ap.av.getAlignment();
1652       }
1653       return als;
1654     }
1655     if (viewport != null)
1656     {
1657       return new AlignmentI[] { viewport.getAlignment() };
1658     }
1659     return null;
1660   }
1661
1662   /**
1663    * DOCUMENT ME!
1664    *
1665    * @param e
1666    *          DOCUMENT ME!
1667    */
1668   @Override
1669   protected void undoMenuItem_actionPerformed(ActionEvent e)
1670   {
1671     if (viewport.getHistoryList().isEmpty())
1672     {
1673       return;
1674     }
1675     CommandI command = viewport.getHistoryList().pop();
1676     viewport.addToRedoList(command);
1677     command.undoCommand(getViewAlignments());
1678
1679     AlignmentViewport originalSource = getOriginatingSource(command);
1680     updateEditMenuBar();
1681
1682     if (originalSource != null)
1683     {
1684       if (originalSource != viewport)
1685       {
1686         Cache.log.warn(
1687                 "Implementation worry: mismatch of viewport origin for undo");
1688       }
1689       originalSource.updateHiddenColumns();
1690       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1691       // null
1692       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1693       // viewport.getColumnSelection()
1694       // .getHiddenColumns().size() > 0);
1695       originalSource.firePropertyChange("alignment", null,
1696               originalSource.getAlignment().getSequences());
1697     }
1698   }
1699
1700   /**
1701    * DOCUMENT ME!
1702    *
1703    * @param e
1704    *          DOCUMENT ME!
1705    */
1706   @Override
1707   protected void redoMenuItem_actionPerformed(ActionEvent e)
1708   {
1709     if (viewport.getRedoList().size() < 1)
1710     {
1711       return;
1712     }
1713
1714     CommandI command = viewport.getRedoList().pop();
1715     viewport.addToHistoryList(command);
1716     command.doCommand(getViewAlignments());
1717
1718     AlignmentViewport originalSource = getOriginatingSource(command);
1719     updateEditMenuBar();
1720
1721     if (originalSource != null)
1722     {
1723
1724       if (originalSource != viewport)
1725       {
1726         Cache.log.warn(
1727                 "Implementation worry: mismatch of viewport origin for redo");
1728       }
1729       originalSource.updateHiddenColumns();
1730       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1731       // null
1732       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1733       // viewport.getColumnSelection()
1734       // .getHiddenColumns().size() > 0);
1735       originalSource.firePropertyChange("alignment", null,
1736               originalSource.getAlignment().getSequences());
1737     }
1738   }
1739
1740   AlignmentViewport getOriginatingSource(CommandI command)
1741   {
1742     AlignmentViewport originalSource = null;
1743     // For sequence removal and addition, we need to fire
1744     // the property change event FROM the viewport where the
1745     // original alignment was altered
1746     AlignmentI al = null;
1747     if (command instanceof EditCommand)
1748     {
1749       EditCommand editCommand = (EditCommand) command;
1750       al = editCommand.getAlignment();
1751       List<Component> comps = PaintRefresher.components
1752               .get(viewport.getSequenceSetId());
1753
1754       for (Component comp : comps)
1755       {
1756         if (comp instanceof AlignmentPanel)
1757         {
1758           if (al == ((AlignmentPanel) comp).av.getAlignment())
1759           {
1760             originalSource = ((AlignmentPanel) comp).av;
1761             break;
1762           }
1763         }
1764       }
1765     }
1766
1767     if (originalSource == null)
1768     {
1769       // The original view is closed, we must validate
1770       // the current view against the closed view first
1771       if (al != null)
1772       {
1773         PaintRefresher.validateSequences(al, viewport.getAlignment());
1774       }
1775
1776       originalSource = viewport;
1777     }
1778
1779     return originalSource;
1780   }
1781
1782   /**
1783    * DOCUMENT ME!
1784    *
1785    * @param up
1786    *          DOCUMENT ME!
1787    */
1788   public void moveSelectedSequences(boolean up)
1789   {
1790     SequenceGroup sg = viewport.getSelectionGroup();
1791
1792     if (sg == null)
1793     {
1794       return;
1795     }
1796     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1797             viewport.getHiddenRepSequences(), up);
1798     alignPanel.paintAlignment(true, false);
1799   }
1800
1801   synchronized void slideSequences(boolean right, int size)
1802   {
1803     List<SequenceI> sg = new ArrayList<>();
1804     if (viewport.cursorMode)
1805     {
1806       sg.add(viewport.getAlignment()
1807               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1808     }
1809     else if (viewport.getSelectionGroup() != null
1810             && viewport.getSelectionGroup().getSize() != viewport
1811                     .getAlignment().getHeight())
1812     {
1813       sg = viewport.getSelectionGroup()
1814               .getSequences(viewport.getHiddenRepSequences());
1815     }
1816
1817     if (sg.size() < 1)
1818     {
1819       return;
1820     }
1821
1822     List<SequenceI> invertGroup = new ArrayList<>();
1823
1824     for (SequenceI seq : viewport.getAlignment().getSequences())
1825     {
1826       if (!sg.contains(seq))
1827       {
1828         invertGroup.add(seq);
1829       }
1830     }
1831
1832     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1833
1834     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1835     for (int i = 0; i < invertGroup.size(); i++)
1836     {
1837       seqs2[i] = invertGroup.get(i);
1838     }
1839
1840     SlideSequencesCommand ssc;
1841     if (right)
1842     {
1843       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1844               viewport.getGapCharacter());
1845     }
1846     else
1847     {
1848       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1849               viewport.getGapCharacter());
1850     }
1851
1852     int groupAdjustment = 0;
1853     if (ssc.getGapsInsertedBegin() && right)
1854     {
1855       if (viewport.cursorMode)
1856       {
1857         alignPanel.getSeqPanel().moveCursor(size, 0);
1858       }
1859       else
1860       {
1861         groupAdjustment = size;
1862       }
1863     }
1864     else if (!ssc.getGapsInsertedBegin() && !right)
1865     {
1866       if (viewport.cursorMode)
1867       {
1868         alignPanel.getSeqPanel().moveCursor(-size, 0);
1869       }
1870       else
1871       {
1872         groupAdjustment = -size;
1873       }
1874     }
1875
1876     if (groupAdjustment != 0)
1877     {
1878       viewport.getSelectionGroup().setStartRes(
1879               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1880       viewport.getSelectionGroup().setEndRes(
1881               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1882     }
1883
1884     /*
1885      * just extend the last slide command if compatible; but not if in
1886      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1887      */
1888     boolean appendHistoryItem = false;
1889     Deque<CommandI> historyList = viewport.getHistoryList();
1890     boolean inSplitFrame = getSplitViewContainer() != null;
1891     if (!inSplitFrame && historyList != null && historyList.size() > 0
1892             && historyList.peek() instanceof SlideSequencesCommand)
1893     {
1894       appendHistoryItem = ssc.appendSlideCommand(
1895               (SlideSequencesCommand) historyList.peek());
1896     }
1897
1898     if (!appendHistoryItem)
1899     {
1900       addHistoryItem(ssc);
1901     }
1902
1903     repaint();
1904   }
1905
1906   /**
1907    * DOCUMENT ME!
1908    *
1909    * @param e
1910    *          DOCUMENT ME!
1911    */
1912   @Override
1913   protected void copy_actionPerformed()
1914   {
1915     if (viewport.getSelectionGroup() == null)
1916     {
1917       return;
1918     }
1919     // TODO: preserve the ordering of displayed alignment annotation in any
1920     // internal paste (particularly sequence associated annotation)
1921     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1922     String[] omitHidden = null;
1923
1924     if (viewport.hasHiddenColumns())
1925     {
1926       omitHidden = viewport.getViewAsString(true);
1927     }
1928
1929     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1930             seqs, omitHidden, null);
1931
1932     StringSelection ss = new StringSelection(output);
1933
1934     Desktop d = Instance.getDesktop();
1935     try
1936     {
1937       d.internalCopy = true;
1938       // Its really worth setting the clipboard contents
1939       // to empty before setting the large StringSelection!!
1940       Toolkit.getDefaultToolkit().getSystemClipboard()
1941               .setContents(new StringSelection(""), null);
1942
1943       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1944               Instance.getDesktop());
1945     } catch (OutOfMemoryError er)
1946     {
1947       new OOMWarning("copying region", er);
1948       return;
1949     }
1950
1951     HiddenColumns hiddenColumns = null;
1952     if (viewport.hasHiddenColumns())
1953     {
1954       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1955       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1956
1957       // create new HiddenColumns object with copy of hidden regions
1958       // between startRes and endRes, offset by startRes
1959       hiddenColumns = new HiddenColumns(
1960               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1961               hiddenCutoff, hiddenOffset);
1962     }
1963
1964     d.jalviewClipboard = new Object[] { seqs,
1965         viewport.getAlignment().getDataset(), hiddenColumns };
1966     setStatus(MessageManager.formatMessage(
1967             "label.copied_sequences_to_clipboard", new Object[]
1968             { Integer.valueOf(seqs.length).toString() }));
1969   }
1970
1971   /**
1972    * DOCUMENT ME!
1973    *
1974    * @param e
1975    *          DOCUMENT ME!
1976    */
1977   @Override
1978   protected void pasteNew_actionPerformed(ActionEvent e)
1979   {
1980     paste(true);
1981   }
1982
1983   /**
1984    * DOCUMENT ME!
1985    *
1986    * @param e
1987    *          DOCUMENT ME!
1988    */
1989   @Override
1990   protected void pasteThis_actionPerformed(ActionEvent e)
1991   {
1992     paste(false);
1993   }
1994
1995   /**
1996    * Paste contents of Jalview clipboard
1997    *
1998    * @param newAlignment
1999    *          true to paste to a new alignment, otherwise add to this.
2000    */
2001   void paste(boolean newAlignment)
2002   {
2003     boolean externalPaste = true;
2004     try
2005     {
2006       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2007       Transferable contents = c.getContents(this);
2008
2009       if (contents == null)
2010       {
2011         return;
2012       }
2013
2014       String str;
2015       FileFormatI format;
2016       try
2017       {
2018         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2019         if (str.length() < 1)
2020         {
2021           return;
2022         }
2023
2024         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2025
2026       } catch (OutOfMemoryError er)
2027       {
2028         new OOMWarning("Out of memory pasting sequences!!", er);
2029         return;
2030       }
2031
2032       SequenceI[] sequences;
2033       boolean annotationAdded = false;
2034       AlignmentI alignment = null;
2035
2036       Desktop d = Instance.getDesktop();
2037
2038       if (d.jalviewClipboard != null)
2039       {
2040         // The clipboard was filled from within Jalview, we must use the
2041         // sequences
2042         // And dataset from the copied alignment
2043         SequenceI[] newseq = (SequenceI[]) d.jalviewClipboard[0];
2044         // be doubly sure that we create *new* sequence objects.
2045         sequences = new SequenceI[newseq.length];
2046         for (int i = 0; i < newseq.length; i++)
2047         {
2048           sequences[i] = new Sequence(newseq[i]);
2049         }
2050         alignment = new Alignment(sequences);
2051         externalPaste = false;
2052       }
2053       else
2054       {
2055         // parse the clipboard as an alignment.
2056         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2057                 format);
2058         sequences = alignment.getSequencesArray();
2059       }
2060
2061       int alwidth = 0;
2062       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2063       int fgroup = -1;
2064
2065       if (newAlignment)
2066       {
2067
2068         if (d.jalviewClipboard != null)
2069         {
2070           // dataset is inherited
2071           alignment.setDataset((Alignment) d.jalviewClipboard[1]);
2072         }
2073         else
2074         {
2075           // new dataset is constructed
2076           alignment.setDataset(null);
2077         }
2078         alwidth = alignment.getWidth() + 1;
2079       }
2080       else
2081       {
2082         AlignmentI pastedal = alignment; // preserve pasted alignment object
2083         // Add pasted sequences and dataset into existing alignment.
2084         alignment = viewport.getAlignment();
2085         alwidth = alignment.getWidth() + 1;
2086         // decide if we need to import sequences from an existing dataset
2087         boolean importDs = d.jalviewClipboard != null
2088                 && d.jalviewClipboard[1] != alignment.getDataset();
2089         // importDs==true instructs us to copy over new dataset sequences from
2090         // an existing alignment
2091         Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
2092                                                                       // create
2093         // minimum dataset set
2094
2095         for (int i = 0; i < sequences.length; i++)
2096         {
2097           if (importDs)
2098           {
2099             newDs.addElement(null);
2100           }
2101           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2102           // paste
2103           if (importDs && ds != null)
2104           {
2105             if (!newDs.contains(ds))
2106             {
2107               newDs.setElementAt(ds, i);
2108               ds = new Sequence(ds);
2109               // update with new dataset sequence
2110               sequences[i].setDatasetSequence(ds);
2111             }
2112             else
2113             {
2114               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2115             }
2116           }
2117           else
2118           {
2119             // copy and derive new dataset sequence
2120             sequences[i] = sequences[i].deriveSequence();
2121             alignment.getDataset()
2122                     .addSequence(sequences[i].getDatasetSequence());
2123             // TODO: avoid creation of duplicate dataset sequences with a
2124             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2125           }
2126           alignment.addSequence(sequences[i]); // merges dataset
2127         }
2128         if (newDs != null)
2129         {
2130           newDs.clear(); // tidy up
2131         }
2132         if (alignment.getAlignmentAnnotation() != null)
2133         {
2134           for (AlignmentAnnotation alan : alignment
2135                   .getAlignmentAnnotation())
2136           {
2137             if (alan.graphGroup > fgroup)
2138             {
2139               fgroup = alan.graphGroup;
2140             }
2141           }
2142         }
2143         if (pastedal.getAlignmentAnnotation() != null)
2144         {
2145           // Add any annotation attached to alignment.
2146           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2147           for (int i = 0; i < alann.length; i++)
2148           {
2149             annotationAdded = true;
2150             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2151             {
2152               AlignmentAnnotation newann = new AlignmentAnnotation(
2153                       alann[i]);
2154               if (newann.graphGroup > -1)
2155               {
2156                 if (newGraphGroups.size() <= newann.graphGroup
2157                         || newGraphGroups.get(newann.graphGroup) == null)
2158                 {
2159                   for (int q = newGraphGroups
2160                           .size(); q <= newann.graphGroup; q++)
2161                   {
2162                     newGraphGroups.add(q, null);
2163                   }
2164                   newGraphGroups.set(newann.graphGroup,
2165                           new Integer(++fgroup));
2166                 }
2167                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2168                         .intValue();
2169               }
2170
2171               newann.padAnnotation(alwidth);
2172               alignment.addAnnotation(newann);
2173             }
2174           }
2175         }
2176       }
2177       if (!newAlignment)
2178       {
2179         // /////
2180         // ADD HISTORY ITEM
2181         //
2182         addHistoryItem(new EditCommand(
2183                 MessageManager.getString("label.add_sequences"),
2184                 Action.PASTE, sequences, 0, alignment.getWidth(),
2185                 alignment));
2186       }
2187       // Add any annotations attached to sequences
2188       for (int i = 0; i < sequences.length; i++)
2189       {
2190         if (sequences[i].getAnnotation() != null)
2191         {
2192           AlignmentAnnotation newann;
2193           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2194           {
2195             annotationAdded = true;
2196             newann = sequences[i].getAnnotation()[a];
2197             newann.adjustForAlignment();
2198             newann.padAnnotation(alwidth);
2199             if (newann.graphGroup > -1)
2200             {
2201               if (newann.graphGroup > -1)
2202               {
2203                 if (newGraphGroups.size() <= newann.graphGroup
2204                         || newGraphGroups.get(newann.graphGroup) == null)
2205                 {
2206                   for (int q = newGraphGroups
2207                           .size(); q <= newann.graphGroup; q++)
2208                   {
2209                     newGraphGroups.add(q, null);
2210                   }
2211                   newGraphGroups.set(newann.graphGroup,
2212                           new Integer(++fgroup));
2213                 }
2214                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2215                         .intValue();
2216               }
2217             }
2218             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2219             // was
2220             // duplicated
2221             // earlier
2222             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2223                     a);
2224           }
2225         }
2226       }
2227       if (!newAlignment)
2228       {
2229
2230         // propagate alignment changed.
2231         viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
2232         if (annotationAdded)
2233         {
2234           // Duplicate sequence annotation in all views.
2235           AlignmentI[] alview = this.getViewAlignments();
2236           for (int i = 0; i < sequences.length; i++)
2237           {
2238             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2239             if (sann == null)
2240             {
2241               continue;
2242             }
2243             for (int avnum = 0; avnum < alview.length; avnum++)
2244             {
2245               if (alview[avnum] != alignment)
2246               {
2247                 // duplicate in a view other than the one with input focus
2248                 int avwidth = alview[avnum].getWidth() + 1;
2249                 // this relies on sann being preserved after we
2250                 // modify the sequence's annotation array for each duplication
2251                 for (int a = 0; a < sann.length; a++)
2252                 {
2253                   AlignmentAnnotation newann = new AlignmentAnnotation(
2254                           sann[a]);
2255                   sequences[i].addAlignmentAnnotation(newann);
2256                   newann.padAnnotation(avwidth);
2257                   alview[avnum].addAnnotation(newann); // annotation was
2258                   // duplicated earlier
2259                   // TODO JAL-1145 graphGroups are not updated for sequence
2260                   // annotation added to several views. This may cause
2261                   // strangeness
2262                   alview[avnum].setAnnotationIndex(newann, a);
2263                 }
2264               }
2265             }
2266           }
2267           buildSortByAnnotationScoresMenu();
2268         }
2269         viewport.firePropertyChange("alignment", null,
2270                 alignment.getSequences());
2271         if (alignPanels != null)
2272         {
2273           for (AlignmentPanel ap : alignPanels)
2274           {
2275             ap.validateAnnotationDimensions(false);
2276           }
2277         }
2278         else
2279         {
2280           alignPanel.validateAnnotationDimensions(false);
2281         }
2282
2283       }
2284       else
2285       {
2286         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2287                 DEFAULT_HEIGHT);
2288         String newtitle = new String("Copied sequences");
2289
2290         if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null)
2291         {
2292           HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2];
2293           af.viewport.setHiddenColumns(hc);
2294         }
2295
2296         // >>>This is a fix for the moment, until a better solution is
2297         // found!!<<<
2298         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2299                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2300                         .getFeatureRenderer());
2301
2302         // TODO: maintain provenance of an alignment, rather than just make the
2303         // title a concatenation of operations.
2304         if (!externalPaste)
2305         {
2306           if (title.startsWith("Copied sequences"))
2307           {
2308             newtitle = title;
2309           }
2310           else
2311           {
2312             newtitle = newtitle.concat("- from " + title);
2313           }
2314         }
2315         else
2316         {
2317           newtitle = new String("Pasted sequences");
2318         }
2319
2320         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2321                 DEFAULT_HEIGHT);
2322
2323       }
2324
2325     } catch (Exception ex)
2326     {
2327       ex.printStackTrace();
2328       System.out.println("Exception whilst pasting: " + ex);
2329       // could be anything being pasted in here
2330     }
2331
2332   }
2333
2334   @Override
2335   protected void expand_newalign(ActionEvent e)
2336   {
2337     try
2338     {
2339       AlignmentI alignment = AlignmentUtils
2340               .expandContext(getViewport().getAlignment(), -1);
2341       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2342               DEFAULT_HEIGHT);
2343       String newtitle = new String("Flanking alignment");
2344
2345       Desktop d = Instance.getDesktop();
2346
2347       if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null)
2348       {
2349         HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2];
2350         af.viewport.setHiddenColumns(hc);
2351       }
2352
2353       // >>>This is a fix for the moment, until a better solution is
2354       // found!!<<<
2355       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2356               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2357                       .getFeatureRenderer());
2358
2359       // TODO: maintain provenance of an alignment, rather than just make the
2360       // title a concatenation of operations.
2361       {
2362         if (title.startsWith("Copied sequences"))
2363         {
2364           newtitle = title;
2365         }
2366         else
2367         {
2368           newtitle = newtitle.concat("- from " + title);
2369         }
2370       }
2371
2372       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2373
2374     } catch (Exception ex)
2375     {
2376       ex.printStackTrace();
2377       System.out.println("Exception whilst pasting: " + ex);
2378       // could be anything being pasted in here
2379     } catch (OutOfMemoryError oom)
2380     {
2381       new OOMWarning("Viewing flanking region of alignment", oom);
2382     }
2383   }
2384
2385   /**
2386    * Action Cut (delete and copy) the selected region
2387    */
2388   @Override
2389   protected void cut_actionPerformed()
2390   {
2391     copy_actionPerformed();
2392     delete_actionPerformed();
2393   }
2394
2395   /**
2396    * Performs menu option to Delete the currently selected region
2397    */
2398   @Override
2399   protected void delete_actionPerformed()
2400   {
2401
2402     SequenceGroup sg = viewport.getSelectionGroup();
2403     if (sg == null)
2404     {
2405       return;
2406     }
2407
2408     Runnable okAction = new Runnable()
2409     {
2410                 @Override
2411                 public void run()
2412                 {
2413                     SequenceI[] cut = sg.getSequences()
2414                             .toArray(new SequenceI[sg.getSize()]);
2415
2416                     addHistoryItem(new EditCommand(
2417                             MessageManager.getString("label.cut_sequences"), Action.CUT,
2418                             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2419                             viewport.getAlignment()));
2420
2421                     viewport.setSelectionGroup(null);
2422                     viewport.sendSelection();
2423                     viewport.getAlignment().deleteGroup(sg);
2424
2425                     viewport.firePropertyChange("alignment", null,
2426                             viewport.getAlignment().getSequences());
2427                     if (viewport.getAlignment().getHeight() < 1)
2428                     {
2429                       try
2430                       {
2431                         AlignFrame.this.setClosed(true);
2432                       } catch (Exception ex)
2433                       {
2434                       }
2435                     }
2436                 }};
2437
2438     /*
2439      * If the cut affects all sequences, prompt for confirmation
2440      */
2441     boolean wholeHeight = sg.getSize() == viewport.getAlignment().getHeight();
2442     boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2443             + 1) == viewport.getAlignment().getWidth()) ? true : false;
2444         if (wholeHeight && wholeWidth)
2445         {
2446             JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane());
2447                 dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2448             Object[] options = new Object[] { MessageManager.getString("action.ok"),
2449                     MessageManager.getString("action.cancel") };
2450                 dialog.showDialog(MessageManager.getString("warn.delete_all"),
2451                     MessageManager.getString("label.delete_all"),
2452                     JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2453                     options, options[0]);
2454         } else
2455         {
2456                 okAction.run();
2457         }
2458   }
2459
2460   /**
2461    * DOCUMENT ME!
2462    *
2463    * @param e
2464    *          DOCUMENT ME!
2465    */
2466   @Override
2467   protected void deleteGroups_actionPerformed(ActionEvent e)
2468   {
2469     if (avc.deleteGroups())
2470     {
2471       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2472       alignPanel.updateAnnotation();
2473       alignPanel.paintAlignment(true, true);
2474     }
2475   }
2476
2477   /**
2478    * DOCUMENT ME!
2479    *
2480    * @param e
2481    *          DOCUMENT ME!
2482    */
2483   @Override
2484   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2485   {
2486     SequenceGroup sg = new SequenceGroup(
2487             viewport.getAlignment().getSequences());
2488
2489     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2490     viewport.setSelectionGroup(sg);
2491     viewport.isSelectionGroupChanged(true);
2492     viewport.sendSelection();
2493     // JAL-2034 - should delegate to
2494     // alignPanel to decide if overview needs
2495     // updating.
2496     alignPanel.paintAlignment(false, false);
2497     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2498   }
2499
2500   /**
2501    * DOCUMENT ME!
2502    *
2503    * @param e
2504    *          DOCUMENT ME!
2505    */
2506   @Override
2507   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2508   {
2509     if (viewport.cursorMode)
2510     {
2511       alignPanel.getSeqPanel().keyboardNo1 = null;
2512       alignPanel.getSeqPanel().keyboardNo2 = null;
2513     }
2514     viewport.setSelectionGroup(null);
2515     viewport.getColumnSelection().clear();
2516     viewport.setSelectionGroup(null);
2517     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2518     // JAL-2034 - should delegate to
2519     // alignPanel to decide if overview needs
2520     // updating.
2521     alignPanel.paintAlignment(false, false);
2522     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2523     viewport.sendSelection();
2524   }
2525
2526   /**
2527    * DOCUMENT ME!
2528    *
2529    * @param e
2530    *          DOCUMENT ME!
2531    */
2532   @Override
2533   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2534   {
2535     SequenceGroup sg = viewport.getSelectionGroup();
2536
2537     if (sg == null)
2538     {
2539       selectAllSequenceMenuItem_actionPerformed(null);
2540
2541       return;
2542     }
2543
2544     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2545     {
2546       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2547     }
2548     // JAL-2034 - should delegate to
2549     // alignPanel to decide if overview needs
2550     // updating.
2551
2552     alignPanel.paintAlignment(true, false);
2553     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2554     viewport.sendSelection();
2555   }
2556
2557   @Override
2558   public void invertColSel_actionPerformed(ActionEvent e)
2559   {
2560     viewport.invertColumnSelection();
2561     alignPanel.paintAlignment(true, false);
2562     viewport.sendSelection();
2563   }
2564
2565   /**
2566    * DOCUMENT ME!
2567    *
2568    * @param e
2569    *          DOCUMENT ME!
2570    */
2571   @Override
2572   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2573   {
2574     trimAlignment(true);
2575   }
2576
2577   /**
2578    * DOCUMENT ME!
2579    *
2580    * @param e
2581    *          DOCUMENT ME!
2582    */
2583   @Override
2584   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2585   {
2586     trimAlignment(false);
2587   }
2588
2589   void trimAlignment(boolean trimLeft)
2590   {
2591     ColumnSelection colSel = viewport.getColumnSelection();
2592     int column;
2593
2594     if (!colSel.isEmpty())
2595     {
2596       if (trimLeft)
2597       {
2598         column = colSel.getMin();
2599       }
2600       else
2601       {
2602         column = colSel.getMax();
2603       }
2604
2605       SequenceI[] seqs;
2606       if (viewport.getSelectionGroup() != null)
2607       {
2608         seqs = viewport.getSelectionGroup()
2609                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2610       }
2611       else
2612       {
2613         seqs = viewport.getAlignment().getSequencesArray();
2614       }
2615
2616       TrimRegionCommand trimRegion;
2617       if (trimLeft)
2618       {
2619         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2620                 column, viewport.getAlignment());
2621         viewport.getRanges().setStartRes(0);
2622       }
2623       else
2624       {
2625         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2626                 column, viewport.getAlignment());
2627       }
2628
2629       setStatus(MessageManager
2630               .formatMessage("label.removed_columns", new String[]
2631               { Integer.valueOf(trimRegion.getSize()).toString() }));
2632
2633       addHistoryItem(trimRegion);
2634
2635       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2636       {
2637         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2638                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2639         {
2640           viewport.getAlignment().deleteGroup(sg);
2641         }
2642       }
2643
2644       viewport.firePropertyChange("alignment", null,
2645               viewport.getAlignment().getSequences());
2646     }
2647   }
2648
2649   /**
2650    * DOCUMENT ME!
2651    *
2652    * @param e
2653    *          DOCUMENT ME!
2654    */
2655   @Override
2656   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2657   {
2658     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2659
2660     SequenceI[] seqs;
2661     if (viewport.getSelectionGroup() != null)
2662     {
2663       seqs = viewport.getSelectionGroup()
2664               .getSequencesAsArray(viewport.getHiddenRepSequences());
2665       start = viewport.getSelectionGroup().getStartRes();
2666       end = viewport.getSelectionGroup().getEndRes();
2667     }
2668     else
2669     {
2670       seqs = viewport.getAlignment().getSequencesArray();
2671     }
2672
2673     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2674             "Remove Gapped Columns", seqs, start, end,
2675             viewport.getAlignment());
2676
2677     addHistoryItem(removeGapCols);
2678
2679     setStatus(MessageManager
2680             .formatMessage("label.removed_empty_columns", new Object[]
2681             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2682
2683     // This is to maintain viewport position on first residue
2684     // of first sequence
2685     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2686     ViewportRanges ranges = viewport.getRanges();
2687     int startRes = seq.findPosition(ranges.getStartRes());
2688     // ShiftList shifts;
2689     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2690     // edit.alColumnChanges=shifts.getInverse();
2691     // if (viewport.hasHiddenColumns)
2692     // viewport.getColumnSelection().compensateForEdits(shifts);
2693     ranges.setStartRes(seq.findIndex(startRes) - 1);
2694     viewport.firePropertyChange("alignment", null,
2695             viewport.getAlignment().getSequences());
2696
2697   }
2698
2699   /**
2700    * DOCUMENT ME!
2701    *
2702    * @param e
2703    *          DOCUMENT ME!
2704    */
2705   @Override
2706   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2707   {
2708     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2709
2710     SequenceI[] seqs;
2711     if (viewport.getSelectionGroup() != null)
2712     {
2713       seqs = viewport.getSelectionGroup()
2714               .getSequencesAsArray(viewport.getHiddenRepSequences());
2715       start = viewport.getSelectionGroup().getStartRes();
2716       end = viewport.getSelectionGroup().getEndRes();
2717     }
2718     else
2719     {
2720       seqs = viewport.getAlignment().getSequencesArray();
2721     }
2722
2723     // This is to maintain viewport position on first residue
2724     // of first sequence
2725     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2726     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2727
2728     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2729             viewport.getAlignment()));
2730
2731     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2732
2733     viewport.firePropertyChange("alignment", null,
2734             viewport.getAlignment().getSequences());
2735
2736   }
2737
2738   /**
2739    * DOCUMENT ME!
2740    *
2741    * @param e
2742    *          DOCUMENT ME!
2743    */
2744   @Override
2745   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2746   {
2747     viewport.setPadGaps(padGapsMenuitem.isSelected());
2748     viewport.firePropertyChange("alignment", null,
2749             viewport.getAlignment().getSequences());
2750   }
2751
2752   /**
2753    * DOCUMENT ME!
2754    *
2755    * @param e
2756    *          DOCUMENT ME!
2757    */
2758   @Override
2759   public void findMenuItem_actionPerformed(ActionEvent e)
2760   {
2761     new Finder();
2762   }
2763
2764   /**
2765    * Create a new view of the current alignment.
2766    */
2767   @Override
2768   public void newView_actionPerformed(ActionEvent e)
2769   {
2770     newView(null, true);
2771   }
2772
2773   /**
2774    * Creates and shows a new view of the current alignment.
2775    *
2776    * @param viewTitle
2777    *          title of newly created view; if null, one will be generated
2778    * @param copyAnnotation
2779    *          if true then duplicate all annnotation, groups and settings
2780    * @return new alignment panel, already displayed.
2781    */
2782   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2783   {
2784     /*
2785      * Create a new AlignmentPanel (with its own, new Viewport)
2786      */
2787     AlignmentPanel newap = new jalview.project.Jalview2XML()
2788             .copyAlignPanel(alignPanel);
2789     if (!copyAnnotation)
2790     {
2791       /*
2792        * remove all groups and annotation except for the automatic stuff
2793        */
2794       newap.av.getAlignment().deleteAllGroups();
2795       newap.av.getAlignment().deleteAllAnnotations(false);
2796     }
2797
2798     newap.av.setGatherViewsHere(false);
2799
2800     if (viewport.getViewName() == null)
2801     {
2802       viewport.setViewName(MessageManager
2803               .getString("label.view_name_original"));
2804     }
2805
2806     /*
2807      * Views share the same edits undo and redo stacks
2808      */
2809     newap.av.setHistoryList(viewport.getHistoryList());
2810     newap.av.setRedoList(viewport.getRedoList());
2811
2812     /*
2813      * copy any visualisation settings that are not saved in the project
2814      */
2815     newap.av.setColourAppliesToAllGroups(
2816             viewport.getColourAppliesToAllGroups());
2817
2818     /*
2819      * Views share the same mappings; need to deregister any new mappings
2820      * created by copyAlignPanel, and register the new reference to the shared
2821      * mappings
2822      */
2823     newap.av.replaceMappings(viewport.getAlignment());
2824
2825     /*
2826      * start up cDNA consensus (if applicable) now mappings are in place
2827      */
2828     if (newap.av.initComplementConsensus())
2829     {
2830       newap.refresh(true); // adjust layout of annotations
2831     }
2832
2833     newap.av.setViewName(getNewViewName(viewTitle));
2834
2835     addAlignmentPanel(newap, true);
2836     newap.alignmentChanged();
2837
2838     if (alignPanels.size() == 2)
2839     {
2840       viewport.setGatherViewsHere(true);
2841     }
2842     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2843     return newap;
2844   }
2845
2846   /**
2847    * Make a new name for the view, ensuring it is unique within the current
2848    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2849    * these now use viewId. Unique view names are still desirable for usability.)
2850    *
2851    * @param viewTitle
2852    * @return
2853    */
2854   protected String getNewViewName(String viewTitle)
2855   {
2856     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2857     boolean addFirstIndex = false;
2858     if (viewTitle == null || viewTitle.trim().length() == 0)
2859     {
2860       viewTitle = MessageManager.getString("action.view");
2861       addFirstIndex = true;
2862     }
2863     else
2864     {
2865       index = 1;// we count from 1 if given a specific name
2866     }
2867     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2868
2869     List<Component> comps = PaintRefresher.components
2870             .get(viewport.getSequenceSetId());
2871
2872     List<String> existingNames = getExistingViewNames(comps);
2873
2874     while (existingNames.contains(newViewName))
2875     {
2876       newViewName = viewTitle + " " + (++index);
2877     }
2878     return newViewName;
2879   }
2880
2881   /**
2882    * Returns a list of distinct view names found in the given list of
2883    * components. View names are held on the viewport of an AlignmentPanel.
2884    *
2885    * @param comps
2886    * @return
2887    */
2888   protected List<String> getExistingViewNames(List<Component> comps)
2889   {
2890     List<String> existingNames = new ArrayList<>();
2891     for (Component comp : comps)
2892     {
2893       if (comp instanceof AlignmentPanel)
2894       {
2895         AlignmentPanel ap = (AlignmentPanel) comp;
2896         if (!existingNames.contains(ap.av.getViewName()))
2897         {
2898           existingNames.add(ap.av.getViewName());
2899         }
2900       }
2901     }
2902     return existingNames;
2903   }
2904
2905   /**
2906    * Explode tabbed views into separate windows.
2907    */
2908   @Override
2909   public void expandViews_actionPerformed(ActionEvent e)
2910   {
2911     Desktop.explodeViews(this);
2912   }
2913
2914   /**
2915    * Gather views in separate windows back into a tabbed presentation.
2916    */
2917   @Override
2918   public void gatherViews_actionPerformed(ActionEvent e)
2919   {
2920     Instance.getDesktop().gatherViews(this);
2921   }
2922
2923   /**
2924    * DOCUMENT ME!
2925    *
2926    * @param e
2927    *          DOCUMENT ME!
2928    */
2929   @Override
2930   public void font_actionPerformed(ActionEvent e)
2931   {
2932     new FontChooser(alignPanel);
2933   }
2934
2935   /**
2936    * DOCUMENT ME!
2937    *
2938    * @param e
2939    *          DOCUMENT ME!
2940    */
2941   @Override
2942   protected void seqLimit_actionPerformed(ActionEvent e)
2943   {
2944     viewport.setShowJVSuffix(seqLimits.isSelected());
2945
2946     alignPanel.getIdPanel().getIdCanvas()
2947             .setPreferredSize(alignPanel.calculateIdWidth());
2948     alignPanel.paintAlignment(true, false);
2949   }
2950
2951   @Override
2952   public void idRightAlign_actionPerformed(ActionEvent e)
2953   {
2954     viewport.setRightAlignIds(idRightAlign.isSelected());
2955     alignPanel.paintAlignment(false, false);
2956   }
2957
2958   @Override
2959   public void centreColumnLabels_actionPerformed(ActionEvent e)
2960   {
2961     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2962     alignPanel.paintAlignment(false, false);
2963   }
2964
2965   /*
2966    * (non-Javadoc)
2967    *
2968    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2969    */
2970   @Override
2971   protected void followHighlight_actionPerformed()
2972   {
2973     /*
2974      * Set the 'follow' flag on the Viewport (and scroll to position if now
2975      * true).
2976      */
2977     final boolean state = this.followHighlightMenuItem.getState();
2978     viewport.setFollowHighlight(state);
2979     if (state)
2980     {
2981       alignPanel.scrollToPosition(viewport.getSearchResults());
2982     }
2983   }
2984
2985   /**
2986    * DOCUMENT ME!
2987    *
2988    * @param e
2989    *          DOCUMENT ME!
2990    */
2991   @Override
2992   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2993   {
2994     viewport.setColourText(colourTextMenuItem.isSelected());
2995     alignPanel.paintAlignment(false, false);
2996   }
2997
2998   /**
2999    * DOCUMENT ME!
3000    *
3001    * @param e
3002    *          DOCUMENT ME!
3003    */
3004   @Override
3005   public void wrapMenuItem_actionPerformed(ActionEvent e)
3006   {
3007     scaleAbove.setVisible(wrapMenuItem.isSelected());
3008     scaleLeft.setVisible(wrapMenuItem.isSelected());
3009     scaleRight.setVisible(wrapMenuItem.isSelected());
3010     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3011     alignPanel.updateLayout();
3012   }
3013
3014   @Override
3015   public void showAllSeqs_actionPerformed(ActionEvent e)
3016   {
3017     viewport.showAllHiddenSeqs();
3018   }
3019
3020   @Override
3021   public void showAllColumns_actionPerformed(ActionEvent e)
3022   {
3023     viewport.showAllHiddenColumns();
3024     alignPanel.paintAlignment(true, true);
3025     viewport.sendSelection();
3026   }
3027
3028   @Override
3029   public void hideSelSequences_actionPerformed(ActionEvent e)
3030   {
3031     viewport.hideAllSelectedSeqs();
3032   }
3033
3034   /**
3035    * called by key handler and the hide all/show all menu items
3036    *
3037    * @param toggleSeqs
3038    * @param toggleCols
3039    */
3040   protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3041   {
3042
3043     boolean hide = false;
3044     SequenceGroup sg = viewport.getSelectionGroup();
3045     if (!toggleSeqs && !toggleCols)
3046     {
3047       // Hide everything by the current selection - this is a hack - we do the
3048       // invert and then hide
3049       // first check that there will be visible columns after the invert.
3050       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3051               && sg.getStartRes() <= sg.getEndRes()))
3052       {
3053         // now invert the sequence set, if required - empty selection implies
3054         // that no hiding is required.
3055         if (sg != null)
3056         {
3057           invertSequenceMenuItem_actionPerformed(null);
3058           sg = viewport.getSelectionGroup();
3059           toggleSeqs = true;
3060
3061         }
3062         viewport.expandColSelection(sg, true);
3063         // finally invert the column selection and get the new sequence
3064         // selection.
3065         invertColSel_actionPerformed(null);
3066         toggleCols = true;
3067       }
3068     }
3069
3070     if (toggleSeqs)
3071     {
3072       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3073       {
3074         hideSelSequences_actionPerformed(null);
3075         hide = true;
3076       }
3077       else if (!(toggleCols && viewport.hasSelectedColumns()))
3078       {
3079         showAllSeqs_actionPerformed(null);
3080       }
3081     }
3082
3083     if (toggleCols)
3084     {
3085       if (viewport.hasSelectedColumns())
3086       {
3087         hideSelColumns_actionPerformed(null);
3088         if (!toggleSeqs)
3089         {
3090           viewport.setSelectionGroup(sg);
3091         }
3092       }
3093       else if (!hide)
3094       {
3095         showAllColumns_actionPerformed(null);
3096       }
3097     }
3098   }
3099
3100   /*
3101    * (non-Javadoc)
3102    *
3103    * @see
3104    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3105    * event.ActionEvent)
3106    */
3107   @Override
3108   public void hideAllButSelection_actionPerformed(ActionEvent e)
3109   {
3110     toggleHiddenRegions(false, false);
3111     viewport.sendSelection();
3112   }
3113
3114   /*
3115    * (non-Javadoc)
3116    *
3117    * @see
3118    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3119    * .ActionEvent)
3120    */
3121   @Override
3122   public void hideAllSelection_actionPerformed(ActionEvent e)
3123   {
3124     SequenceGroup sg = viewport.getSelectionGroup();
3125     viewport.expandColSelection(sg, false);
3126     viewport.hideAllSelectedSeqs();
3127     viewport.hideSelectedColumns();
3128     alignPanel.updateLayout();
3129     alignPanel.paintAlignment(true, true);
3130     viewport.sendSelection();
3131   }
3132
3133   /*
3134    * (non-Javadoc)
3135    *
3136    * @see
3137    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3138    * ActionEvent)
3139    */
3140   @Override
3141   public void showAllhidden_actionPerformed(ActionEvent e)
3142   {
3143     viewport.showAllHiddenColumns();
3144     viewport.showAllHiddenSeqs();
3145     alignPanel.paintAlignment(true, true);
3146     viewport.sendSelection();
3147   }
3148
3149   @Override
3150   public void hideSelColumns_actionPerformed(ActionEvent e)
3151   {
3152     viewport.hideSelectedColumns();
3153     alignPanel.updateLayout();
3154     alignPanel.paintAlignment(true, true);
3155     viewport.sendSelection();
3156   }
3157
3158   @Override
3159   public void hiddenMarkers_actionPerformed(ActionEvent e)
3160   {
3161     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3162     repaint();
3163   }
3164
3165   /**
3166    * DOCUMENT ME!
3167    *
3168    * @param e
3169    *          DOCUMENT ME!
3170    */
3171   @Override
3172   protected void scaleAbove_actionPerformed(ActionEvent e)
3173   {
3174     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3175     alignPanel.updateLayout();
3176     alignPanel.paintAlignment(true, false);
3177   }
3178
3179   /**
3180    * DOCUMENT ME!
3181    *
3182    * @param e
3183    *          DOCUMENT ME!
3184    */
3185   @Override
3186   protected void scaleLeft_actionPerformed(ActionEvent e)
3187   {
3188     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3189     alignPanel.updateLayout();
3190     alignPanel.paintAlignment(true, false);
3191   }
3192
3193   /**
3194    * DOCUMENT ME!
3195    *
3196    * @param e
3197    *          DOCUMENT ME!
3198    */
3199   @Override
3200   protected void scaleRight_actionPerformed(ActionEvent e)
3201   {
3202     viewport.setScaleRightWrapped(scaleRight.isSelected());
3203     alignPanel.updateLayout();
3204     alignPanel.paintAlignment(true, false);
3205   }
3206
3207   /**
3208    * DOCUMENT ME!
3209    *
3210    * @param e
3211    *          DOCUMENT ME!
3212    */
3213   @Override
3214   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3215   {
3216     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3217     alignPanel.paintAlignment(false, false);
3218   }
3219
3220   /**
3221    * DOCUMENT ME!
3222    *
3223    * @param e
3224    *          DOCUMENT ME!
3225    */
3226   @Override
3227   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3228   {
3229     viewport.setShowText(viewTextMenuItem.isSelected());
3230     alignPanel.paintAlignment(false, false);
3231   }
3232
3233   /**
3234    * DOCUMENT ME!
3235    *
3236    * @param e
3237    *          DOCUMENT ME!
3238    */
3239   @Override
3240   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3241   {
3242     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3243     alignPanel.paintAlignment(false, false);
3244   }
3245
3246   public FeatureSettings featureSettings;
3247
3248   @Override
3249   public FeatureSettingsControllerI getFeatureSettingsUI()
3250   {
3251     return featureSettings;
3252   }
3253
3254   @Override
3255   public void featureSettings_actionPerformed(ActionEvent e)
3256   {
3257     if (featureSettings != null)
3258     {
3259       featureSettings.close();
3260       featureSettings = null;
3261     }
3262     if (!showSeqFeatures.isSelected())
3263     {
3264       // make sure features are actually displayed
3265       showSeqFeatures.setSelected(true);
3266       showSeqFeatures_actionPerformed(null);
3267     }
3268     featureSettings = new FeatureSettings(this);
3269   }
3270
3271   /**
3272    * Set or clear 'Show Sequence Features'
3273    *
3274    * @param evt
3275    *          DOCUMENT ME!
3276    */
3277   @Override
3278   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3279   {
3280     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3281     alignPanel.paintAlignment(true, true);
3282   }
3283
3284   /**
3285    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3286    * the annotations panel as a whole.
3287    *
3288    * The options to show/hide all annotations should be enabled when the panel
3289    * is shown, and disabled when the panel is hidden.
3290    *
3291    * @param e
3292    */
3293   @Override
3294   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3295   {
3296     final boolean setVisible = annotationPanelMenuItem.isSelected();
3297     viewport.setShowAnnotation(setVisible);
3298     this.showAllSeqAnnotations.setEnabled(setVisible);
3299     this.hideAllSeqAnnotations.setEnabled(setVisible);
3300     this.showAllAlAnnotations.setEnabled(setVisible);
3301     this.hideAllAlAnnotations.setEnabled(setVisible);
3302     alignPanel.updateLayout();
3303   }
3304
3305   @Override
3306   public void alignmentProperties()
3307   {
3308     JComponent pane;
3309     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3310
3311             .formatAsHtml();
3312     String content = MessageManager.formatMessage("label.html_content",
3313             new Object[]
3314             { contents.toString() });
3315     contents = null;
3316
3317     if (Platform.isJS())
3318     {
3319       JLabel textLabel = new JLabel();
3320       textLabel.setText(content);
3321       textLabel.setBackground(Color.WHITE);
3322
3323       pane = new JPanel(new BorderLayout());
3324       ((JPanel) pane).setOpaque(true);
3325       pane.setBackground(Color.WHITE);
3326       ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3327     }
3328     else
3329     /**
3330      * Java only
3331      *
3332      * @j2sIgnore
3333      */
3334     {
3335       JEditorPane editPane = new JEditorPane("text/html", "");
3336       editPane.setEditable(false);
3337       editPane.setText(content);
3338       pane = editPane;
3339     }
3340
3341     JInternalFrame frame = new JInternalFrame();
3342
3343     frame.getContentPane().add(new JScrollPane(pane));
3344
3345     Desktop.addInternalFrame(frame, MessageManager
3346             .formatMessage("label.alignment_properties", new Object[]
3347             { getTitle() }), 500, 400);
3348   }
3349
3350   /**
3351    * DOCUMENT ME!
3352    *
3353    * @param e
3354    *          DOCUMENT ME!
3355    */
3356   @Override
3357   public void overviewMenuItem_actionPerformed(ActionEvent e)
3358   {
3359     if (alignPanel.overviewPanel != null)
3360     {
3361       return;
3362     }
3363
3364     JInternalFrame frame = new JInternalFrame();
3365     final OverviewPanel overview = new OverviewPanel(alignPanel);
3366     frame.setContentPane(overview);
3367     Desktop.addInternalFrame(frame, MessageManager
3368             .formatMessage("label.overview_params", new Object[]
3369             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3370             true, true);
3371     frame.pack();
3372     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3373     frame.addInternalFrameListener(
3374             new javax.swing.event.InternalFrameAdapter()
3375             {
3376               @Override
3377               public void internalFrameClosed(
3378                       javax.swing.event.InternalFrameEvent evt)
3379               {
3380                 overview.dispose();
3381                 alignPanel.setOverviewPanel(null);
3382               }
3383             });
3384     if (getKeyListeners().length > 0)
3385     {
3386       frame.addKeyListener(getKeyListeners()[0]);
3387     }
3388
3389     alignPanel.setOverviewPanel(overview);
3390   }
3391
3392   @Override
3393   public void textColour_actionPerformed()
3394   {
3395     new TextColourChooser().chooseColour(alignPanel, null);
3396   }
3397
3398   /*
3399    * public void covariationColour_actionPerformed() {
3400    * changeColour(new
3401    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3402    * ()[0])); }
3403    */
3404   @Override
3405   public void annotationColour_actionPerformed()
3406   {
3407     new AnnotationColourChooser(viewport, alignPanel);
3408   }
3409
3410   @Override
3411   public void annotationColumn_actionPerformed(ActionEvent e)
3412   {
3413     new AnnotationColumnChooser(viewport, alignPanel);
3414   }
3415
3416   /**
3417    * Action on the user checking or unchecking the option to apply the selected
3418    * colour scheme to all groups. If unchecked, groups may have their own
3419    * independent colour schemes.
3420    *
3421    * @param selected
3422    */
3423   @Override
3424   public void applyToAllGroups_actionPerformed(boolean selected)
3425   {
3426     viewport.setColourAppliesToAllGroups(selected);
3427   }
3428
3429   /**
3430    * Action on user selecting a colour from the colour menu
3431    *
3432    * @param name
3433    *          the name (not the menu item label!) of the colour scheme
3434    */
3435   @Override
3436   public void changeColour_actionPerformed(String name)
3437   {
3438     /*
3439      * 'User Defined' opens a panel to configure or load a
3440      * user-defined colour scheme
3441      */
3442     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3443     {
3444       new UserDefinedColours(alignPanel);
3445       return;
3446     }
3447
3448     /*
3449      * otherwise set the chosen colour scheme (or null for 'None')
3450      */
3451     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3452             viewport,
3453             viewport.getAlignment(), viewport.getHiddenRepSequences());
3454     changeColour(cs);
3455   }
3456
3457   /**
3458    * Actions on setting or changing the alignment colour scheme
3459    *
3460    * @param cs
3461    */
3462   @Override
3463   public void changeColour(ColourSchemeI cs)
3464   {
3465     // TODO: pull up to controller method
3466     ColourMenuHelper.setColourSelected(colourMenu, cs);
3467
3468     viewport.setGlobalColourScheme(cs);
3469
3470     alignPanel.paintAlignment(true, true);
3471   }
3472
3473   /**
3474    * Show the PID threshold slider panel
3475    */
3476   @Override
3477   protected void modifyPID_actionPerformed()
3478   {
3479     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3480             alignPanel.getViewName());
3481     SliderPanel.showPIDSlider();
3482   }
3483
3484   /**
3485    * Show the Conservation slider panel
3486    */
3487   @Override
3488   protected void modifyConservation_actionPerformed()
3489   {
3490     SliderPanel.setConservationSlider(alignPanel,
3491             viewport.getResidueShading(), alignPanel.getViewName());
3492     SliderPanel.showConservationSlider();
3493   }
3494
3495   /**
3496    * Action on selecting or deselecting (Colour) By Conservation
3497    */
3498   @Override
3499   public void conservationMenuItem_actionPerformed(boolean selected)
3500   {
3501     modifyConservation.setEnabled(selected);
3502     viewport.setConservationSelected(selected);
3503     viewport.getResidueShading().setConservationApplied(selected);
3504
3505     changeColour(viewport.getGlobalColourScheme());
3506     if (selected)
3507     {
3508       modifyConservation_actionPerformed();
3509     }
3510     else
3511     {
3512       SliderPanel.hideConservationSlider();
3513     }
3514   }
3515
3516   /**
3517    * Action on selecting or deselecting (Colour) Above PID Threshold
3518    */
3519   @Override
3520   public void abovePIDThreshold_actionPerformed(boolean selected)
3521   {
3522     modifyPID.setEnabled(selected);
3523     viewport.setAbovePIDThreshold(selected);
3524     if (!selected)
3525     {
3526       viewport.getResidueShading().setThreshold(0,
3527               viewport.isIgnoreGapsConsensus());
3528     }
3529
3530     changeColour(viewport.getGlobalColourScheme());
3531     if (selected)
3532     {
3533       modifyPID_actionPerformed();
3534     }
3535     else
3536     {
3537       SliderPanel.hidePIDSlider();
3538     }
3539   }
3540
3541   /**
3542    * DOCUMENT ME!
3543    *
3544    * @param e
3545    *          DOCUMENT ME!
3546    */
3547   @Override
3548   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3549   {
3550     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3551     AlignmentSorter.sortByPID(viewport.getAlignment(),
3552             viewport.getAlignment().getSequenceAt(0));
3553     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3554             viewport.getAlignment()));
3555     alignPanel.paintAlignment(true, false);
3556   }
3557
3558   /**
3559    * DOCUMENT ME!
3560    *
3561    * @param e
3562    *          DOCUMENT ME!
3563    */
3564   @Override
3565   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3566   {
3567     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3568     AlignmentSorter.sortByID(viewport.getAlignment());
3569     addHistoryItem(
3570             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3571     alignPanel.paintAlignment(true, false);
3572   }
3573
3574   /**
3575    * DOCUMENT ME!
3576    *
3577    * @param e
3578    *          DOCUMENT ME!
3579    */
3580   @Override
3581   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3582   {
3583     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3584     AlignmentSorter.sortByLength(viewport.getAlignment());
3585     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3586             viewport.getAlignment()));
3587     alignPanel.paintAlignment(true, false);
3588   }
3589
3590   /**
3591    * DOCUMENT ME!
3592    *
3593    * @param e
3594    *          DOCUMENT ME!
3595    */
3596   @Override
3597   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3598   {
3599     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3600     AlignmentSorter.sortByGroup(viewport.getAlignment());
3601     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3602             viewport.getAlignment()));
3603
3604     alignPanel.paintAlignment(true, false);
3605   }
3606
3607   /**
3608    * DOCUMENT ME!
3609    *
3610    * @param e
3611    *          DOCUMENT ME!
3612    */
3613   @Override
3614   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3615   {
3616     new RedundancyPanel(alignPanel, this);
3617   }
3618
3619   /**
3620    * DOCUMENT ME!
3621    *
3622    * @param e
3623    *          DOCUMENT ME!
3624    */
3625   @Override
3626   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3627   {
3628     if ((viewport.getSelectionGroup() == null)
3629             || (viewport.getSelectionGroup().getSize() < 2))
3630     {
3631       JvOptionPane.showInternalMessageDialog(this,
3632               MessageManager.getString(
3633                       "label.you_must_select_least_two_sequences"),
3634               MessageManager.getString("label.invalid_selection"),
3635               JvOptionPane.WARNING_MESSAGE);
3636     }
3637     else
3638     {
3639       JInternalFrame frame = new JInternalFrame();
3640       frame.setContentPane(new PairwiseAlignPanel(viewport));
3641       Desktop.addInternalFrame(frame,
3642               MessageManager.getString("action.pairwise_alignment"), 600,
3643               500);
3644     }
3645   }
3646
3647   @Override
3648   public void autoCalculate_actionPerformed(ActionEvent e)
3649   {
3650     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3651     if (viewport.autoCalculateConsensus)
3652     {
3653       viewport.firePropertyChange("alignment", null,
3654               viewport.getAlignment().getSequences());
3655     }
3656   }
3657
3658   @Override
3659   public void sortByTreeOption_actionPerformed(ActionEvent e)
3660   {
3661     viewport.sortByTree = sortByTree.isSelected();
3662   }
3663
3664   @Override
3665   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3666   {
3667     viewport.followSelection = listenToViewSelections.isSelected();
3668   }
3669
3670   /**
3671    * Constructs a tree panel and adds it to the desktop
3672    *
3673    * @param type
3674    *          tree type (NJ or AV)
3675    * @param modelName
3676    *          name of score model used to compute the tree
3677    * @param options
3678    *          parameters for the distance or similarity calculation
3679    */
3680   void newTreePanel(String type, String modelName,
3681           SimilarityParamsI options)
3682   {
3683     String frameTitle = "";
3684     TreePanel tp;
3685
3686     boolean onSelection = false;
3687     if (viewport.getSelectionGroup() != null
3688             && viewport.getSelectionGroup().getSize() > 0)
3689     {
3690       SequenceGroup sg = viewport.getSelectionGroup();
3691
3692       /* Decide if the selection is a column region */
3693       for (SequenceI _s : sg.getSequences())
3694       {
3695         if (_s.getLength() < sg.getEndRes())
3696         {
3697           JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
3698                   MessageManager.getString(
3699                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3700                   MessageManager.getString(
3701                           "label.sequences_selection_not_aligned"),
3702                   JvOptionPane.WARNING_MESSAGE);
3703
3704           return;
3705         }
3706       }
3707       onSelection = true;
3708     }
3709     else
3710     {
3711       if (viewport.getAlignment().getHeight() < 2)
3712       {
3713         return;
3714       }
3715     }
3716
3717     tp = new TreePanel(alignPanel, type, modelName, options);
3718     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3719
3720     frameTitle += " from ";
3721
3722     if (viewport.getViewName() != null)
3723     {
3724       frameTitle += viewport.getViewName() + " of ";
3725     }
3726
3727     frameTitle += this.title;
3728
3729     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3730   }
3731
3732   /**
3733    * DOCUMENT ME!
3734    *
3735    * @param title
3736    *          DOCUMENT ME!
3737    * @param order
3738    *          DOCUMENT ME!
3739    */
3740   public void addSortByOrderMenuItem(String title,
3741           final AlignmentOrder order)
3742   {
3743     final JMenuItem item = new JMenuItem(MessageManager
3744             .formatMessage("action.by_title_param", new Object[]
3745             { title }));
3746     sort.add(item);
3747     item.addActionListener(new java.awt.event.ActionListener()
3748     {
3749       @Override
3750       public void actionPerformed(ActionEvent e)
3751       {
3752         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3753
3754         // TODO: JBPNote - have to map order entries to curent SequenceI
3755         // pointers
3756         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3757
3758         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3759                 viewport.getAlignment()));
3760
3761         alignPanel.paintAlignment(true, false);
3762       }
3763     });
3764   }
3765
3766   /**
3767    * Add a new sort by annotation score menu item
3768    *
3769    * @param sort
3770    *          the menu to add the option to
3771    * @param scoreLabel
3772    *          the label used to retrieve scores for each sequence on the
3773    *          alignment
3774    */
3775   public void addSortByAnnotScoreMenuItem(JMenu sort,
3776           final String scoreLabel)
3777   {
3778     final JMenuItem item = new JMenuItem(scoreLabel);
3779     sort.add(item);
3780     item.addActionListener(new java.awt.event.ActionListener()
3781     {
3782       @Override
3783       public void actionPerformed(ActionEvent e)
3784       {
3785         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3786         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3787                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3788         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3789                 viewport.getAlignment()));
3790         alignPanel.paintAlignment(true, false);
3791       }
3792     });
3793   }
3794
3795   /**
3796    * last hash for alignment's annotation array - used to minimise cost of
3797    * rebuild.
3798    */
3799   protected int _annotationScoreVectorHash;
3800
3801   /**
3802    * search the alignment and rebuild the sort by annotation score submenu the
3803    * last alignment annotation vector hash is stored to minimize cost of
3804    * rebuilding in subsequence calls.
3805    *
3806    */
3807   @Override
3808   public void buildSortByAnnotationScoresMenu()
3809   {
3810     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3811     {
3812       return;
3813     }
3814
3815     if (viewport.getAlignment().getAlignmentAnnotation()
3816             .hashCode() != _annotationScoreVectorHash)
3817     {
3818       sortByAnnotScore.removeAll();
3819       // almost certainly a quicker way to do this - but we keep it simple
3820       Hashtable<String, String> scoreSorts = new Hashtable<>();
3821       AlignmentAnnotation aann[];
3822       for (SequenceI sqa : viewport.getAlignment().getSequences())
3823       {
3824         aann = sqa.getAnnotation();
3825         for (int i = 0; aann != null && i < aann.length; i++)
3826         {
3827           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3828           {
3829             scoreSorts.put(aann[i].label, aann[i].label);
3830           }
3831         }
3832       }
3833       Enumeration<String> labels = scoreSorts.keys();
3834       while (labels.hasMoreElements())
3835       {
3836         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3837                 labels.nextElement());
3838       }
3839       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3840       scoreSorts.clear();
3841
3842       _annotationScoreVectorHash = viewport.getAlignment()
3843               .getAlignmentAnnotation().hashCode();
3844     }
3845   }
3846
3847   /**
3848    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3849    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3850    * call. Listeners are added to remove the menu item when the treePanel is
3851    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3852    * modified.
3853    */
3854   @Override
3855   public void buildTreeSortMenu()
3856   {
3857     sortByTreeMenu.removeAll();
3858
3859     List<Component> comps = PaintRefresher.components
3860             .get(viewport.getSequenceSetId());
3861     List<TreePanel> treePanels = new ArrayList<>();
3862     for (Component comp : comps)
3863     {
3864       if (comp instanceof TreePanel)
3865       {
3866         treePanels.add((TreePanel) comp);
3867       }
3868     }
3869
3870     if (treePanels.size() < 1)
3871     {
3872       sortByTreeMenu.setVisible(false);
3873       return;
3874     }
3875
3876     sortByTreeMenu.setVisible(true);
3877
3878     for (final TreePanel tp : treePanels)
3879     {
3880       final JMenuItem item = new JMenuItem(tp.getTitle());
3881       item.addActionListener(new java.awt.event.ActionListener()
3882       {
3883         @Override
3884         public void actionPerformed(ActionEvent e)
3885         {
3886           tp.sortByTree_actionPerformed();
3887           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3888
3889         }
3890       });
3891
3892       sortByTreeMenu.add(item);
3893     }
3894   }
3895
3896   public boolean sortBy(AlignmentOrder alorder, String undoname)
3897   {
3898     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3899     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3900     if (undoname != null)
3901     {
3902       addHistoryItem(new OrderCommand(undoname, oldOrder,
3903               viewport.getAlignment()));
3904     }
3905     alignPanel.paintAlignment(true, false);
3906     return true;
3907   }
3908
3909   /**
3910    * Work out whether the whole set of sequences or just the selected set will
3911    * be submitted for multiple alignment.
3912    *
3913    */
3914   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3915   {
3916     // Now, check we have enough sequences
3917     AlignmentView msa = null;
3918
3919     if ((viewport.getSelectionGroup() != null)
3920             && (viewport.getSelectionGroup().getSize() > 1))
3921     {
3922       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3923       // some common interface!
3924       /*
3925        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3926        * SequenceI[sz = seqs.getSize(false)];
3927        *
3928        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3929        * seqs.getSequenceAt(i); }
3930        */
3931       msa = viewport.getAlignmentView(true);
3932     }
3933     else if (viewport.getSelectionGroup() != null
3934             && viewport.getSelectionGroup().getSize() == 1)
3935     {
3936       int option = JvOptionPane.showConfirmDialog(this,
3937               MessageManager.getString("warn.oneseq_msainput_selection"),
3938               MessageManager.getString("label.invalid_selection"),
3939               JvOptionPane.OK_CANCEL_OPTION);
3940       if (option == JvOptionPane.OK_OPTION)
3941       {
3942         msa = viewport.getAlignmentView(false);
3943       }
3944     }
3945     else
3946     {
3947       msa = viewport.getAlignmentView(false);
3948     }
3949     return msa;
3950   }
3951
3952   /**
3953    * Decides what is submitted to a secondary structure prediction service: the
3954    * first sequence in the alignment, or in the current selection, or, if the
3955    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3956    * region or the whole alignment. (where the first sequence in the set is the
3957    * one that the prediction will be for).
3958    */
3959   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3960   {
3961     AlignmentView seqs = null;
3962
3963     if ((viewport.getSelectionGroup() != null)
3964             && (viewport.getSelectionGroup().getSize() > 0))
3965     {
3966       seqs = viewport.getAlignmentView(true);
3967     }
3968     else
3969     {
3970       seqs = viewport.getAlignmentView(false);
3971     }
3972     // limit sequences - JBPNote in future - could spawn multiple prediction
3973     // jobs
3974     // TODO: viewport.getAlignment().isAligned is a global state - the local
3975     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3976     if (!viewport.getAlignment().isAligned(false))
3977     {
3978       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3979       // TODO: if seqs.getSequences().length>1 then should really have warned
3980       // user!
3981
3982     }
3983     return seqs;
3984   }
3985
3986   /**
3987    * DOCUMENT ME!
3988    *
3989    * @param e
3990    *          DOCUMENT ME!
3991    */
3992   @Override
3993   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3994   {
3995     // Pick the tree file
3996     JalviewFileChooser chooser = new JalviewFileChooser(
3997             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3998     chooser.setFileView(new JalviewFileView());
3999     chooser.setDialogTitle(
4000             MessageManager.getString("label.select_newick_like_tree_file"));
4001     chooser.setToolTipText(
4002             MessageManager.getString("label.load_tree_file"));
4003
4004     chooser.setResponseHandler(0,new Runnable()
4005     {
4006       @Override
4007       public void run()
4008       {
4009         String filePath = chooser.getSelectedFile().getPath();
4010         Cache.setProperty("LAST_DIRECTORY", filePath);
4011         NewickFile fin = null;
4012         try
4013         {
4014           fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
4015                   DataSourceType.FILE));
4016           viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4017         } catch (Exception ex)
4018         {
4019           JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), ex.getMessage(),
4020                   MessageManager
4021                           .getString("label.problem_reading_tree_file"),
4022                   JvOptionPane.WARNING_MESSAGE);
4023           ex.printStackTrace();
4024         }
4025         if (fin != null && fin.hasWarningMessage())
4026         {
4027           JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
4028                   fin.getWarningMessage(),
4029                   MessageManager.getString(
4030                           "label.possible_problem_with_tree_file"),
4031                   JvOptionPane.WARNING_MESSAGE);
4032         }
4033       }
4034     });
4035     chooser.showOpenDialog(this);
4036   }
4037
4038   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4039   {
4040     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4041   }
4042
4043   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4044           int h, int x, int y)
4045   {
4046     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4047   }
4048
4049   /**
4050    * Add a treeviewer for the tree extracted from a Newick file object to the
4051    * current alignment view
4052    *
4053    * @param nf
4054    *          the tree
4055    * @param title
4056    *          tree viewer title
4057    * @param input
4058    *          Associated alignment input data (or null)
4059    * @param w
4060    *          width
4061    * @param h
4062    *          height
4063    * @param x
4064    *          position
4065    * @param y
4066    *          position
4067    * @return TreePanel handle
4068    */
4069   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4070           AlignmentView input, int w, int h, int x, int y)
4071   {
4072     TreePanel tp = null;
4073
4074     try
4075     {
4076       nf.parse();
4077
4078       if (nf.getTree() != null)
4079       {
4080         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4081
4082         tp.setSize(w, h);
4083
4084         if (x > 0 && y > 0)
4085         {
4086           tp.setLocation(x, y);
4087         }
4088
4089         Desktop.addInternalFrame(tp, treeTitle, w, h);
4090       }
4091     } catch (Exception ex)
4092     {
4093       ex.printStackTrace();
4094     }
4095
4096     return tp;
4097   }
4098
4099   private boolean buildingMenu = false;
4100
4101   /**
4102    * Generates menu items and listener event actions for web service clients
4103    *
4104    */
4105   public void BuildWebServiceMenu()
4106   {
4107     while (buildingMenu)
4108     {
4109       try
4110       {
4111         System.err.println("Waiting for building menu to finish.");
4112         Thread.sleep(10);
4113       } catch (Exception e)
4114       {
4115       }
4116     }
4117     final AlignFrame me = this;
4118     buildingMenu = true;
4119     new Thread(new Runnable()
4120     {
4121       @Override
4122       public void run()
4123       {
4124         final List<JMenuItem> legacyItems = new ArrayList<>();
4125         try
4126         {
4127           // System.err.println("Building ws menu again "
4128           // + Thread.currentThread());
4129           // TODO: add support for context dependent disabling of services based
4130           // on
4131           // alignment and current selection
4132           // TODO: add additional serviceHandle parameter to specify abstract
4133           // handler
4134           // class independently of AbstractName
4135           // TODO: add in rediscovery GUI function to restart discoverer
4136           // TODO: group services by location as well as function and/or
4137           // introduce
4138           // object broker mechanism.
4139           final Vector<JMenu> wsmenu = new Vector<>();
4140           final IProgressIndicator af = me;
4141
4142           /*
4143            * do not i18n these strings - they are hard-coded in class
4144            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4145            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4146            */
4147           final JMenu msawsmenu = new JMenu("Alignment");
4148           final JMenu secstrmenu = new JMenu(
4149                   "Secondary Structure Prediction");
4150           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4151           final JMenu analymenu = new JMenu("Analysis");
4152           final JMenu dismenu = new JMenu("Protein Disorder");
4153           // JAL-940 - only show secondary structure prediction services from
4154           // the legacy server
4155           Hashtable<String, Vector<ServiceHandle>> services = Discoverer
4156                   .getInstance().getServices();
4157           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4158           // &&
4159           services != null && (services.size() > 0))
4160           {
4161             // TODO: refactor to allow list of AbstractName/Handler bindings to
4162             // be
4163             // stored or retrieved from elsewhere
4164             // No MSAWS used any more:
4165             // Vector msaws = null; // (Vector)
4166             // Discoverer.services.get("MsaWS");
4167             Vector<ServiceHandle> secstrpr = services.get("SecStrPred");
4168             if (secstrpr != null)
4169             {
4170               // Add any secondary structure prediction services
4171               for (int i = 0, j = secstrpr.size(); i < j; i++)
4172               {
4173                 final ext.vamsas.ServiceHandle sh = secstrpr
4174                         .get(i);
4175                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4176                         .getServiceClient(sh);
4177                 int p = secstrmenu.getItemCount();
4178                 impl.attachWSMenuEntry(secstrmenu, me);
4179                 int q = secstrmenu.getItemCount();
4180                 for (int litm = p; litm < q; litm++)
4181                 {
4182                   legacyItems.add(secstrmenu.getItem(litm));
4183                 }
4184               }
4185             }
4186           }
4187
4188           // Add all submenus in the order they should appear on the web
4189           // services menu
4190           wsmenu.add(msawsmenu);
4191           wsmenu.add(secstrmenu);
4192           wsmenu.add(dismenu);
4193           wsmenu.add(analymenu);
4194           // No search services yet
4195           // wsmenu.add(seqsrchmenu);
4196
4197           javax.swing.SwingUtilities.invokeLater(new Runnable()
4198           {
4199             @Override
4200             public void run()
4201             {
4202               try
4203               {
4204                 webService.removeAll();
4205                 // first, add discovered services onto the webservices menu
4206                 if (wsmenu.size() > 0)
4207                 {
4208                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4209                   {
4210                     webService.add(wsmenu.get(i));
4211                   }
4212                 }
4213                 else
4214                 {
4215                   webService.add(me.webServiceNoServices);
4216                 }
4217                 // TODO: move into separate menu builder class.
4218                 // boolean new_sspred = false;
4219                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4220                 {
4221                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4222                   if (jws2servs != null)
4223                   {
4224                     if (jws2servs.hasServices())
4225                     {
4226                       jws2servs.attachWSMenuEntry(webService, me);
4227                       for (Jws2Instance sv : jws2servs.getServices())
4228                       {
4229                         if (sv.description.toLowerCase().contains("jpred"))
4230                         {
4231                           for (JMenuItem jmi : legacyItems)
4232                           {
4233                             jmi.setVisible(false);
4234                           }
4235                         }
4236                       }
4237
4238                     }
4239                     if (jws2servs.isRunning())
4240                     {
4241                       JMenuItem tm = new JMenuItem(
4242                               "Still discovering JABA Services");
4243                       tm.setEnabled(false);
4244                       webService.add(tm);
4245                     }
4246                   }
4247                 }
4248                 build_urlServiceMenu(me.webService);
4249                 build_fetchdbmenu(webService);
4250                 for (JMenu item : wsmenu)
4251                 {
4252                   if (item.getItemCount() == 0)
4253                   {
4254                     item.setEnabled(false);
4255                   }
4256                   else
4257                   {
4258                     item.setEnabled(true);
4259                   }
4260                 }
4261               } catch (Exception e)
4262               {
4263                 Cache.log.debug(
4264                         "Exception during web service menu building process.",
4265                         e);
4266               }
4267             }
4268           });
4269         } catch (Exception e)
4270         {
4271         }
4272         buildingMenu = false;
4273       }
4274     }).start();
4275
4276   }
4277
4278   /**
4279    * construct any groupURL type service menu entries.
4280    *
4281    * @param webService
4282    */
4283   protected void build_urlServiceMenu(JMenu webService)
4284   {
4285     // TODO: remove this code when 2.7 is released
4286     // DEBUG - alignmentView
4287     /*
4288      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4289      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4290      *
4291      * @Override public void actionPerformed(ActionEvent e) {
4292      * jalview.datamodel.AlignmentView
4293      * .testSelectionViews(af.viewport.getAlignment(),
4294      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4295      *
4296      * }); webService.add(testAlView);
4297      */
4298     // TODO: refactor to RestClient discoverer and merge menu entries for
4299     // rest-style services with other types of analysis/calculation service
4300     // SHmmr test client - still being implemented.
4301     // DEBUG - alignmentView
4302
4303     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4304             .getRestClients())
4305     {
4306       client.attachWSMenuEntry(
4307               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4308               this);
4309     }
4310   }
4311
4312   /**
4313    * Searches the alignment sequences for xRefs and builds the Show
4314    * Cross-References menu (formerly called Show Products), with database
4315    * sources for which cross-references are found (protein sources for a
4316    * nucleotide alignment and vice versa)
4317    *
4318    * @return true if Show Cross-references menu should be enabled
4319    */
4320   public boolean canShowProducts()
4321   {
4322     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4323     AlignmentI dataset = viewport.getAlignment().getDataset();
4324
4325     showProducts.removeAll();
4326     final boolean dna = viewport.getAlignment().isNucleotide();
4327
4328     if (seqs == null || seqs.length == 0)
4329     {
4330       // nothing to see here.
4331       return false;
4332     }
4333
4334     boolean showp = false;
4335     try
4336     {
4337       List<String> ptypes = new CrossRef(seqs, dataset)
4338               .findXrefSourcesForSequences(dna);
4339
4340       for (final String source : ptypes)
4341       {
4342         showp = true;
4343         final AlignFrame af = this;
4344         JMenuItem xtype = new JMenuItem(source);
4345         xtype.addActionListener(new ActionListener()
4346         {
4347           @Override
4348           public void actionPerformed(ActionEvent e)
4349           {
4350             showProductsFor(af.viewport.getSequenceSelection(), dna,
4351                     source);
4352           }
4353         });
4354         showProducts.add(xtype);
4355       }
4356       showProducts.setVisible(showp);
4357       showProducts.setEnabled(showp);
4358     } catch (Exception e)
4359     {
4360       Cache.log.warn(
4361               "canShowProducts threw an exception - please report to help@jalview.org",
4362               e);
4363       return false;
4364     }
4365     return showp;
4366   }
4367
4368   /**
4369    * Finds and displays cross-references for the selected sequences (protein
4370    * products for nucleotide sequences, dna coding sequences for peptides).
4371    *
4372    * @param sel
4373    *          the sequences to show cross-references for
4374    * @param dna
4375    *          true if from a nucleotide alignment (so showing proteins)
4376    * @param source
4377    *          the database to show cross-references for
4378    */
4379   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4380           final String source)
4381   {
4382     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4383             .start();
4384   }
4385
4386   /**
4387    * Construct and display a new frame containing the translation of this
4388    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4389    */
4390   @Override
4391   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4392   {
4393     AlignmentI al = null;
4394     try
4395     {
4396       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4397
4398       al = dna.translateCdna(codeTable);
4399     } catch (Exception ex)
4400     {
4401       jalview.bin.Cache.log.error(
4402               "Exception during translation. Please report this !", ex);
4403       final String msg = MessageManager.getString(
4404               "label.error_when_translating_sequences_submit_bug_report");
4405       final String errorTitle = MessageManager
4406               .getString("label.implementation_error")
4407               + MessageManager.getString("label.translation_failed");
4408       JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg, errorTitle,
4409               JvOptionPane.ERROR_MESSAGE);
4410       return;
4411     }
4412     if (al == null || al.getHeight() == 0)
4413     {
4414       final String msg = MessageManager.getString(
4415               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4416       final String errorTitle = MessageManager
4417               .getString("label.translation_failed");
4418       JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg, errorTitle,
4419               JvOptionPane.WARNING_MESSAGE);
4420     }
4421     else
4422     {
4423       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4424       af.setFileFormat(this.currentFileFormat);
4425       final String newTitle = MessageManager
4426               .formatMessage("label.translation_of_params", new Object[]
4427               { this.getTitle(), codeTable.getId() });
4428       af.setTitle(newTitle);
4429       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4430       {
4431         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4432         viewport.openSplitFrame(af, new Alignment(seqs));
4433       }
4434       else
4435       {
4436         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4437                 DEFAULT_HEIGHT);
4438       }
4439     }
4440   }
4441
4442   /**
4443    * Set the file format
4444    *
4445    * @param format
4446    */
4447   public void setFileFormat(FileFormatI format)
4448   {
4449     this.currentFileFormat = format;
4450   }
4451
4452   /**
4453    * Try to load a features file onto the alignment.
4454    *
4455    * @param file
4456    *          contents or path to retrieve file or a File object
4457    * @param sourceType
4458    *          access mode of file (see jalview.io.AlignFile)
4459    * @return true if features file was parsed correctly.
4460    */
4461   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4462   {
4463     // BH 2018
4464     return avc.parseFeaturesFile(file, sourceType,
4465             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4466
4467   }
4468
4469   @Override
4470   public void refreshFeatureUI(boolean enableIfNecessary)
4471   {
4472     // note - currently this is only still here rather than in the controller
4473     // because of the featureSettings hard reference that is yet to be
4474     // abstracted
4475     if (enableIfNecessary)
4476     {
4477       viewport.setShowSequenceFeatures(true);
4478       showSeqFeatures.setSelected(true);
4479     }
4480
4481   }
4482
4483   @Override
4484   public void dragEnter(DropTargetDragEvent evt)
4485   {
4486   }
4487
4488   @Override
4489   public void dragExit(DropTargetEvent evt)
4490   {
4491   }
4492
4493   @Override
4494   public void dragOver(DropTargetDragEvent evt)
4495   {
4496   }
4497
4498   @Override
4499   public void dropActionChanged(DropTargetDragEvent evt)
4500   {
4501   }
4502
4503   @Override
4504   public void drop(DropTargetDropEvent evt)
4505   {
4506     // JAL-1552 - acceptDrop required before getTransferable call for
4507     // Java's Transferable for native dnd
4508     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4509     Transferable t = evt.getTransferable();
4510
4511     final AlignFrame thisaf = this;
4512     final List<Object> files = new ArrayList<>();
4513     List<DataSourceType> protocols = new ArrayList<>();
4514
4515     try
4516     {
4517       Desktop.transferFromDropTarget(files, protocols, evt, t);
4518     } catch (Exception e)
4519     {
4520       e.printStackTrace();
4521     }
4522     if (files != null)
4523     {
4524       new Thread(new Runnable()
4525       {
4526         @Override
4527         public void run()
4528         {
4529           try
4530           {
4531             // check to see if any of these files have names matching sequences
4532             // in
4533             // the alignment
4534             SequenceIdMatcher idm = new SequenceIdMatcher(
4535                     viewport.getAlignment().getSequencesArray());
4536             /**
4537              * Object[] { String,SequenceI}
4538              */
4539             ArrayList<Object[]> filesmatched = new ArrayList<>();
4540             ArrayList<Object> filesnotmatched = new ArrayList<>();
4541             for (int i = 0; i < files.size(); i++)
4542             {
4543               // BH 2018
4544               Object file = files.get(i);
4545               String fileName = file.toString();
4546               String pdbfn = "";
4547               DataSourceType protocol = (file instanceof File
4548                       ? DataSourceType.FILE
4549                       : FormatAdapter.checkProtocol(fileName));
4550               if (protocol == DataSourceType.FILE)
4551               {
4552                 File fl;
4553                 if (file instanceof File) {
4554                   fl = (File) file;
4555                   Platform.cacheFileData(fl);
4556                 } else {
4557                   fl = new File(fileName);
4558                 }
4559                 pdbfn = fl.getName();
4560               }
4561               else if (protocol == DataSourceType.URL)
4562               {
4563                 URL url = new URL(fileName);
4564                 pdbfn = url.getFile();
4565               }
4566               if (pdbfn.length() > 0)
4567               {
4568                 // attempt to find a match in the alignment
4569                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4570                 int l = 0, c = pdbfn.indexOf(".");
4571                 while (mtch == null && c != -1)
4572                 {
4573                   do
4574                   {
4575                     l = c;
4576                   } while ((c = pdbfn.indexOf(".", l)) > l);
4577                   if (l > -1)
4578                   {
4579                     pdbfn = pdbfn.substring(0, l);
4580                   }
4581                   mtch = idm.findAllIdMatches(pdbfn);
4582                 }
4583                 if (mtch != null)
4584                 {
4585                   FileFormatI type;
4586                   try
4587                   {
4588                     type = new IdentifyFile().identify(file, protocol);
4589                   } catch (Exception ex)
4590                   {
4591                     type = null;
4592                   }
4593                   if (type != null && type.isStructureFile())
4594                   {
4595                     filesmatched.add(new Object[] { file, protocol, mtch });
4596                     continue;
4597                   }
4598                 }
4599                 // File wasn't named like one of the sequences or wasn't a PDB
4600                 // file.
4601                 filesnotmatched.add(file);
4602               }
4603             }
4604             int assocfiles = 0;
4605             if (filesmatched.size() > 0)
4606             {
4607               boolean autoAssociate = Cache
4608                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4609               if (!autoAssociate)
4610               {
4611                 String msg = MessageManager.formatMessage(
4612                         "label.automatically_associate_structure_files_with_sequences_same_name",
4613                         new Object[]
4614                         { Integer.valueOf(filesmatched.size())
4615                                 .toString() });
4616                 String ttl = MessageManager.getString(
4617                         "label.automatically_associate_structure_files_by_name");
4618                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4619                         ttl, JvOptionPane.YES_NO_OPTION);
4620                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4621               }
4622               if (autoAssociate)
4623               {
4624                 for (Object[] fm : filesmatched)
4625                 {
4626                   // try and associate
4627                   // TODO: may want to set a standard ID naming formalism for
4628                   // associating PDB files which have no IDs.
4629                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4630                   {
4631                     PDBEntry pe = new AssociatePdbFileWithSeq()
4632                             .associatePdbWithSeq(fm[0].toString(),
4633                                     (DataSourceType) fm[1], toassoc, false,
4634                                     Instance.getDesktop());
4635                     if (pe != null)
4636                     {
4637                       System.err.println("Associated file : "
4638                               + (fm[0].toString()) + " with "
4639                               + toassoc.getDisplayId(true));
4640                       assocfiles++;
4641                     }
4642                   }
4643                   // TODO: do we need to update overview ? only if features are
4644                   // shown I guess
4645                   alignPanel.paintAlignment(true, false);
4646                 }
4647               }
4648               else
4649               {
4650                 /*
4651                  * add declined structures as sequences
4652                  */
4653                 for (Object[] o : filesmatched)
4654                 {
4655                   filesnotmatched.add(o[0]);
4656                 }
4657               }
4658             }
4659             if (filesnotmatched.size() > 0)
4660             {
4661               if (assocfiles > 0 && (Cache.getDefault(
4662                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4663                       || JvOptionPane.showConfirmDialog(thisaf,
4664                               "<html>" + MessageManager.formatMessage(
4665                                       "label.ignore_unmatched_dropped_files_info",
4666                                       new Object[]
4667                                       { Integer.valueOf(
4668                                               filesnotmatched.size())
4669                                               .toString() })
4670                                       + "</html>",
4671                               MessageManager.getString(
4672                                       "label.ignore_unmatched_dropped_files"),
4673                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4674               {
4675                 return;
4676               }
4677               for (Object fn : filesnotmatched)
4678               {
4679                 loadJalviewDataFile(fn, null, null, null);
4680               }
4681
4682             }
4683           } catch (Exception ex)
4684           {
4685             ex.printStackTrace();
4686           }
4687         }
4688       }).start();
4689     }
4690   }
4691
4692   /**
4693    * Attempt to load a "dropped" file or URL string, by testing in turn for
4694    * <ul>
4695    * <li>an Annotation file</li>
4696    * <li>a JNet file</li>
4697    * <li>a features file</li>
4698    * <li>else try to interpret as an alignment file</li>
4699    * </ul>
4700    *
4701    * @param file
4702    *          either a filename or a URL string.
4703    */
4704   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4705           FileFormatI format, SequenceI assocSeq)
4706   {
4707     // BH 2018 was String file
4708     try
4709     {
4710       if (sourceType == null)
4711       {
4712         sourceType = FormatAdapter.checkProtocol(file);
4713       }
4714       // if the file isn't identified, or not positively identified as some
4715       // other filetype (PFAM is default unidentified alignment file type) then
4716       // try to parse as annotation.
4717       boolean isAnnotation = (format == null
4718               || FileFormat.Pfam.equals(format))
4719                       ? new AnnotationFile().annotateAlignmentView(viewport,
4720                               file, sourceType)
4721                       : false;
4722
4723       if (!isAnnotation)
4724       {
4725         // first see if its a T-COFFEE score file
4726         TCoffeeScoreFile tcf = null;
4727         try
4728         {
4729           tcf = new TCoffeeScoreFile(file, sourceType);
4730           if (tcf.isValid())
4731           {
4732             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4733             {
4734               buildColourMenu();
4735               changeColour(
4736                       new TCoffeeColourScheme(viewport.getAlignment()));
4737               isAnnotation = true;
4738               setStatus(MessageManager.getString(
4739                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4740             }
4741             else
4742             {
4743               // some problem - if no warning its probable that the ID matching
4744               // process didn't work
4745               JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
4746                       tcf.getWarningMessage() == null
4747                               ? MessageManager.getString(
4748                                       "label.check_file_matches_sequence_ids_alignment")
4749                               : tcf.getWarningMessage(),
4750                       MessageManager.getString(
4751                               "label.problem_reading_tcoffee_score_file"),
4752                       JvOptionPane.WARNING_MESSAGE);
4753             }
4754           }
4755           else
4756           {
4757             tcf = null;
4758           }
4759         } catch (Exception x)
4760         {
4761           Cache.log.debug(
4762                   "Exception when processing data source as T-COFFEE score file",
4763                   x);
4764           tcf = null;
4765         }
4766         if (tcf == null)
4767         {
4768           // try to see if its a JNet 'concise' style annotation file *before*
4769           // we
4770           // try to parse it as a features file
4771           if (format == null)
4772           {
4773             format = new IdentifyFile().identify(file, sourceType);
4774           }
4775           if (FileFormat.ScoreMatrix == format)
4776           {
4777             ScoreMatrixFile sm = new ScoreMatrixFile(
4778                     new FileParse(file, sourceType));
4779             sm.parse();
4780             // todo: i18n this message
4781             setStatus(MessageManager.formatMessage(
4782                     "label.successfully_loaded_matrix",
4783                     sm.getMatrixName()));
4784           }
4785           else if (FileFormat.Jnet.equals(format))
4786           {
4787             JPredFile predictions = new JPredFile(file, sourceType);
4788             new JnetAnnotationMaker();
4789             JnetAnnotationMaker.add_annotation(predictions,
4790                     viewport.getAlignment(), 0, false);
4791             viewport.getAlignment().setupJPredAlignment();
4792             isAnnotation = true;
4793           }
4794           // else if (IdentifyFile.FeaturesFile.equals(format))
4795           else if (FileFormat.Features.equals(format))
4796           {
4797             if (parseFeaturesFile(file, sourceType))
4798             {
4799               alignPanel.paintAlignment(true, true);
4800             }
4801           }
4802           else
4803           {
4804             new FileLoader().LoadFile(viewport, file, sourceType, format);
4805           }
4806         }
4807       }
4808       if (isAnnotation)
4809       {
4810
4811         alignPanel.adjustAnnotationHeight();
4812         viewport.updateSequenceIdColours();
4813         buildSortByAnnotationScoresMenu();
4814         alignPanel.paintAlignment(true, true);
4815       }
4816     } catch (Exception ex)
4817     {
4818       ex.printStackTrace();
4819     } catch (OutOfMemoryError oom)
4820     {
4821       try
4822       {
4823         System.gc();
4824       } catch (Exception x)
4825       {
4826       }
4827       new OOMWarning(
4828               "loading data "
4829                       + (sourceType != null
4830                               ? (sourceType == DataSourceType.PASTE
4831                                       ? "from clipboard."
4832                                       : "using " + sourceType + " from "
4833                                               + file)
4834                               : ".")
4835                       + (format != null
4836                               ? "(parsing as '" + format + "' file)"
4837                               : ""),
4838               oom, Desktop.getDesktopPane());
4839     }
4840   }
4841
4842   /**
4843    * Method invoked by the ChangeListener on the tabbed pane, in other words
4844    * when a different tabbed pane is selected by the user or programmatically.
4845    */
4846   @Override
4847   public void tabSelectionChanged(int index)
4848   {
4849     if (index > -1)
4850     {
4851       alignPanel = alignPanels.get(index);
4852       viewport = alignPanel.av;
4853       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4854       setMenusFromViewport(viewport);
4855     }
4856
4857     /*
4858      * 'focus' any colour slider that is open to the selected viewport
4859      */
4860     if (viewport.getConservationSelected())
4861     {
4862       SliderPanel.setConservationSlider(alignPanel,
4863               viewport.getResidueShading(), alignPanel.getViewName());
4864     }
4865     else
4866     {
4867       SliderPanel.hideConservationSlider();
4868     }
4869     if (viewport.getAbovePIDThreshold())
4870     {
4871       SliderPanel.setPIDSliderSource(alignPanel,
4872               viewport.getResidueShading(), alignPanel.getViewName());
4873     }
4874     else
4875     {
4876       SliderPanel.hidePIDSlider();
4877     }
4878
4879     /*
4880      * If there is a frame linked to this one in a SplitPane, switch it to the
4881      * same view tab index. No infinite recursion of calls should happen, since
4882      * tabSelectionChanged() should not get invoked on setting the selected
4883      * index to an unchanged value. Guard against setting an invalid index
4884      * before the new view peer tab has been created.
4885      */
4886     final AlignViewportI peer = viewport.getCodingComplement();
4887     if (peer != null)
4888     {
4889       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4890               .getAlignPanel().alignFrame;
4891       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4892       {
4893         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4894       }
4895     }
4896   }
4897
4898   /**
4899    * On right mouse click on view tab, prompt for and set new view name.
4900    */
4901   @Override
4902   public void tabbedPane_mousePressed(MouseEvent e)
4903   {
4904     if (e.isPopupTrigger())
4905     {
4906       String msg = MessageManager.getString("label.enter_view_name");
4907       String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
4908       String reply = JvOptionPane.showInputDialog(msg, ttl);
4909
4910       if (reply != null)
4911       {
4912         viewport.setViewName(reply);
4913         // TODO warn if reply is in getExistingViewNames()?
4914         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4915       }
4916     }
4917   }
4918
4919   public AlignViewport getCurrentView()
4920   {
4921     return viewport;
4922   }
4923
4924   /**
4925    * Open the dialog for regex description parsing.
4926    */
4927   @Override
4928   protected void extractScores_actionPerformed(ActionEvent e)
4929   {
4930     ParseProperties pp = new jalview.analysis.ParseProperties(
4931             viewport.getAlignment());
4932     // TODO: verify regex and introduce GUI dialog for version 2.5
4933     // if (pp.getScoresFromDescription("col", "score column ",
4934     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4935     // true)>0)
4936     if (pp.getScoresFromDescription("description column",
4937             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4938     {
4939       buildSortByAnnotationScoresMenu();
4940     }
4941   }
4942
4943   /*
4944    * (non-Javadoc)
4945    *
4946    * @see
4947    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4948    * )
4949    */
4950   @Override
4951   protected void showDbRefs_actionPerformed(ActionEvent e)
4952   {
4953     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4954   }
4955
4956   /*
4957    * (non-Javadoc)
4958    *
4959    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4960    * ActionEvent)
4961    */
4962   @Override
4963   protected void showNpFeats_actionPerformed(ActionEvent e)
4964   {
4965     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4966   }
4967
4968   /**
4969    * find the viewport amongst the tabs in this alignment frame and close that
4970    * tab
4971    *
4972    * @param av
4973    */
4974   public boolean closeView(AlignViewportI av)
4975   {
4976     if (viewport == av)
4977     {
4978       this.closeMenuItem_actionPerformed(false);
4979       return true;
4980     }
4981     Component[] comp = tabbedPane.getComponents();
4982     for (int i = 0; comp != null && i < comp.length; i++)
4983     {
4984       if (comp[i] instanceof AlignmentPanel)
4985       {
4986         if (((AlignmentPanel) comp[i]).av == av)
4987         {
4988           // close the view.
4989           closeView((AlignmentPanel) comp[i]);
4990           return true;
4991         }
4992       }
4993     }
4994     return false;
4995   }
4996
4997   protected void build_fetchdbmenu(JMenu webService)
4998   {
4999     // Temporary hack - DBRef Fetcher always top level ws entry.
5000     // TODO We probably want to store a sequence database checklist in
5001     // preferences and have checkboxes.. rather than individual sources selected
5002     // here
5003     final JMenu rfetch = new JMenu(
5004             MessageManager.getString("action.fetch_db_references"));
5005     rfetch.setToolTipText(MessageManager.getString(
5006             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5007     webService.add(rfetch);
5008
5009     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5010             MessageManager.getString("option.trim_retrieved_seqs"));
5011     trimrs.setToolTipText(
5012             MessageManager.getString("label.trim_retrieved_sequences"));
5013     trimrs.setSelected(
5014             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5015     trimrs.addActionListener(new ActionListener()
5016     {
5017       @Override
5018       public void actionPerformed(ActionEvent e)
5019       {
5020         trimrs.setSelected(trimrs.isSelected());
5021         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5022                 Boolean.valueOf(trimrs.isSelected()).toString());
5023       }
5024     });
5025     rfetch.add(trimrs);
5026     JMenuItem fetchr = new JMenuItem(
5027             MessageManager.getString("label.standard_databases"));
5028     fetchr.setToolTipText(
5029             MessageManager.getString("label.fetch_embl_uniprot"));
5030     fetchr.addActionListener(new ActionListener()
5031     {
5032
5033       @Override
5034       public void actionPerformed(ActionEvent e)
5035       {
5036         new Thread(new Runnable()
5037         {
5038           @Override
5039           public void run()
5040           {
5041             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5042                     .getAlignment().isNucleotide();
5043             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5044                     alignPanel.av.getSequenceSelection(),
5045                     alignPanel.alignFrame, null,
5046                     alignPanel.alignFrame.featureSettings, isNucleotide);
5047             dbRefFetcher.addListener(new FetchFinishedListenerI()
5048             {
5049               @Override
5050               public void finished()
5051               {
5052                 AlignFrame.this.setMenusForViewport();
5053               }
5054             });
5055             dbRefFetcher.fetchDBRefs(false);
5056           }
5057         }).start();
5058
5059       }
5060
5061     });
5062     rfetch.add(fetchr);
5063     new Thread(new Runnable()
5064     {
5065       @Override
5066       public void run()
5067       {
5068         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5069                 .getSequenceFetcherSingleton();
5070         javax.swing.SwingUtilities.invokeLater(new Runnable()
5071         {
5072           @Override
5073           public void run()
5074           {
5075             String[] dbclasses = sf.getNonAlignmentSources();
5076             List<DbSourceProxy> otherdb;
5077             JMenu dfetch = new JMenu();
5078             JMenu ifetch = new JMenu();
5079             JMenuItem fetchr = null;
5080             int comp = 0, icomp = 0, mcomp = 15;
5081             String mname = null;
5082             int dbi = 0;
5083             for (String dbclass : dbclasses)
5084             {
5085               otherdb = sf.getSourceProxy(dbclass);
5086               // add a single entry for this class, or submenu allowing 'fetch
5087               // all' or pick one
5088               if (otherdb == null || otherdb.size() < 1)
5089               {
5090                 continue;
5091               }
5092               if (mname == null)
5093               {
5094                 mname = "From " + dbclass;
5095               }
5096               if (otherdb.size() == 1)
5097               {
5098                 DbSourceProxy src = otherdb.get(0);
5099                 DbSourceProxy[] dassource = new DbSourceProxy[] {
5100                     src };
5101                 fetchr = new JMenuItem(src.getDbSource());
5102                 fetchr.addActionListener(new ActionListener()
5103                 {
5104
5105                   @Override
5106                   public void actionPerformed(ActionEvent e)
5107                   {
5108                     new Thread(new Runnable()
5109                     {
5110
5111                       @Override
5112                       public void run()
5113                       {
5114                         boolean isNucleotide = alignPanel.alignFrame
5115                                 .getViewport().getAlignment()
5116                                 .isNucleotide();
5117                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5118                                 alignPanel.av.getSequenceSelection(),
5119                                 alignPanel.alignFrame, dassource,
5120                                 alignPanel.alignFrame.featureSettings,
5121                                 isNucleotide);
5122                         dbRefFetcher
5123                                 .addListener(new FetchFinishedListenerI()
5124                                 {
5125                                   @Override
5126                                   public void finished()
5127                                   {
5128                                     AlignFrame.this.setMenusForViewport();
5129                                   }
5130                                 });
5131                         dbRefFetcher.fetchDBRefs(false);
5132                       }
5133                     }).start();
5134                   }
5135
5136                 });
5137                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5138                         MessageManager.formatMessage(
5139                                 "label.fetch_retrieve_from", new Object[]
5140                                 { src.getDbName() })));
5141                 dfetch.add(fetchr);
5142                 comp++;
5143               }
5144               else
5145               {
5146                 final DbSourceProxy[] dassource = otherdb
5147                         .toArray(new DbSourceProxy[0]);
5148                 // fetch all entry
5149                 DbSourceProxy src = otherdb.get(0);
5150                 fetchr = new JMenuItem(MessageManager
5151                         .formatMessage("label.fetch_all_param", new Object[]
5152                         { src.getDbSource() }));
5153                 fetchr.addActionListener(new ActionListener()
5154                 {
5155                   @Override
5156                   public void actionPerformed(ActionEvent e)
5157                   {
5158                     new Thread(new Runnable()
5159                     {
5160
5161                       @Override
5162                       public void run()
5163                       {
5164                         boolean isNucleotide = alignPanel.alignFrame
5165                                 .getViewport().getAlignment()
5166                                 .isNucleotide();
5167                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5168                                 alignPanel.av.getSequenceSelection(),
5169                                 alignPanel.alignFrame, dassource,
5170                                 alignPanel.alignFrame.featureSettings,
5171                                 isNucleotide);
5172                         dbRefFetcher
5173                                 .addListener(new FetchFinishedListenerI()
5174                                 {
5175                                   @Override
5176                                   public void finished()
5177                                   {
5178                                     AlignFrame.this.setMenusForViewport();
5179                                   }
5180                                 });
5181                         dbRefFetcher.fetchDBRefs(false);
5182                       }
5183                     }).start();
5184                   }
5185                 });
5186
5187                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5188                         MessageManager.formatMessage(
5189                                 "label.fetch_retrieve_from_all_sources",
5190                                 new Object[]
5191                                 { Integer.valueOf(otherdb.size())
5192                                         .toString(),
5193                                     src.getDbSource(), src.getDbName() })));
5194                 dfetch.add(fetchr);
5195                 comp++;
5196                 // and then build the rest of the individual menus
5197                 ifetch = new JMenu(MessageManager.formatMessage(
5198                         "label.source_from_db_source", new Object[]
5199                         { src.getDbSource() }));
5200                 icomp = 0;
5201                 String imname = null;
5202                 int i = 0;
5203                 for (DbSourceProxy sproxy : otherdb)
5204                 {
5205                   String dbname = sproxy.getDbName();
5206                   String sname = dbname.length() > 5
5207                           ? dbname.substring(0, 5) + "..."
5208                           : dbname;
5209                   String msname = dbname.length() > 10
5210                           ? dbname.substring(0, 10) + "..."
5211                           : dbname;
5212                   if (imname == null)
5213                   {
5214                     imname = MessageManager
5215                             .formatMessage("label.from_msname", new Object[]
5216                             { sname });
5217                   }
5218                   fetchr = new JMenuItem(msname);
5219                   final DbSourceProxy[] dassrc = { sproxy };
5220                   fetchr.addActionListener(new ActionListener()
5221                   {
5222
5223                     @Override
5224                     public void actionPerformed(ActionEvent e)
5225                     {
5226                       new Thread(new Runnable()
5227                       {
5228
5229                         @Override
5230                         public void run()
5231                         {
5232                           boolean isNucleotide = alignPanel.alignFrame
5233                                   .getViewport().getAlignment()
5234                                   .isNucleotide();
5235                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5236                                   alignPanel.av.getSequenceSelection(),
5237                                   alignPanel.alignFrame, dassrc,
5238                                   alignPanel.alignFrame.featureSettings,
5239                                   isNucleotide);
5240                           dbRefFetcher
5241                                   .addListener(new FetchFinishedListenerI()
5242                                   {
5243                                     @Override
5244                                     public void finished()
5245                                     {
5246                                       AlignFrame.this.setMenusForViewport();
5247                                     }
5248                                   });
5249                           dbRefFetcher.fetchDBRefs(false);
5250                         }
5251                       }).start();
5252                     }
5253
5254                   });
5255                   fetchr.setToolTipText(
5256                           "<html>" + MessageManager.formatMessage(
5257                                   "label.fetch_retrieve_from", new Object[]
5258                                   { dbname }));
5259                   ifetch.add(fetchr);
5260                   ++i;
5261                   if (++icomp >= mcomp || i == (otherdb.size()))
5262                   {
5263                     ifetch.setText(MessageManager.formatMessage(
5264                             "label.source_to_target", imname, sname));
5265                     dfetch.add(ifetch);
5266                     ifetch = new JMenu();
5267                     imname = null;
5268                     icomp = 0;
5269                     comp++;
5270                   }
5271                 }
5272               }
5273               ++dbi;
5274               if (comp >= mcomp || dbi >= (dbclasses.length))
5275               {
5276                 dfetch.setText(MessageManager.formatMessage(
5277                         "label.source_to_target", mname, dbclass));
5278                 rfetch.add(dfetch);
5279                 dfetch = new JMenu();
5280                 mname = null;
5281                 comp = 0;
5282               }
5283             }
5284           }
5285         });
5286       }
5287     }).start();
5288
5289   }
5290
5291   /**
5292    * Left justify the whole alignment.
5293    */
5294   @Override
5295   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5296   {
5297     AlignmentI al = viewport.getAlignment();
5298     al.justify(false);
5299     viewport.firePropertyChange("alignment", null, al);
5300   }
5301
5302   /**
5303    * Right justify the whole alignment.
5304    */
5305   @Override
5306   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5307   {
5308     AlignmentI al = viewport.getAlignment();
5309     al.justify(true);
5310     viewport.firePropertyChange("alignment", null, al);
5311   }
5312
5313   @Override
5314   public void setShowSeqFeatures(boolean b)
5315   {
5316     showSeqFeatures.setSelected(b);
5317     viewport.setShowSequenceFeatures(b);
5318   }
5319
5320   /*
5321    * (non-Javadoc)
5322    *
5323    * @see
5324    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5325    * awt.event.ActionEvent)
5326    */
5327   @Override
5328   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5329   {
5330     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5331     alignPanel.paintAlignment(false, false);
5332   }
5333
5334   /*
5335    * (non-Javadoc)
5336    *
5337    * @see
5338    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5339    * .ActionEvent)
5340    */
5341   @Override
5342   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5343   {
5344     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5345     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5346
5347   }
5348
5349   /*
5350    * (non-Javadoc)
5351    *
5352    * @see
5353    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5354    * .event.ActionEvent)
5355    */
5356   @Override
5357   protected void showGroupConservation_actionPerformed(ActionEvent e)
5358   {
5359     viewport.setShowGroupConservation(showGroupConservation.getState());
5360     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5361   }
5362
5363   /*
5364    * (non-Javadoc)
5365    *
5366    * @see
5367    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5368    * .event.ActionEvent)
5369    */
5370   @Override
5371   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5372   {
5373     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5374     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5375   }
5376
5377   /*
5378    * (non-Javadoc)
5379    *
5380    * @see
5381    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5382    * .event.ActionEvent)
5383    */
5384   @Override
5385   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5386   {
5387     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5388     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5389   }
5390
5391   @Override
5392   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5393   {
5394     showSequenceLogo.setState(true);
5395     viewport.setShowSequenceLogo(true);
5396     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5397     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5398   }
5399
5400   @Override
5401   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5402   {
5403     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5404   }
5405
5406   /*
5407    * (non-Javadoc)
5408    *
5409    * @see
5410    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5411    * .event.ActionEvent)
5412    */
5413   @Override
5414   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5415   {
5416     if (avc.makeGroupsFromSelection())
5417     {
5418       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5419       alignPanel.updateAnnotation();
5420       alignPanel.paintAlignment(true,
5421               viewport.needToUpdateStructureViews());
5422     }
5423   }
5424
5425   public void clearAlignmentSeqRep()
5426   {
5427     // TODO refactor alignmentseqrep to controller
5428     if (viewport.getAlignment().hasSeqrep())
5429     {
5430       viewport.getAlignment().setSeqrep(null);
5431       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5432       alignPanel.updateAnnotation();
5433       alignPanel.paintAlignment(true, true);
5434     }
5435   }
5436
5437   @Override
5438   protected void createGroup_actionPerformed(ActionEvent e)
5439   {
5440     if (avc.createGroup())
5441     {
5442       if (applyAutoAnnotationSettings.isSelected())
5443       {
5444         alignPanel.updateAnnotation(true, false);
5445       }
5446       alignPanel.alignmentChanged();
5447     }
5448   }
5449
5450   @Override
5451   protected void unGroup_actionPerformed(ActionEvent e)
5452   {
5453     if (avc.unGroup())
5454     {
5455       alignPanel.alignmentChanged();
5456     }
5457   }
5458
5459   /**
5460    * make the given alignmentPanel the currently selected tab
5461    *
5462    * @param alignmentPanel
5463    */
5464   public void setDisplayedView(AlignmentPanel alignmentPanel)
5465   {
5466     if (!viewport.getSequenceSetId()
5467             .equals(alignmentPanel.av.getSequenceSetId()))
5468     {
5469       throw new Error(MessageManager.getString(
5470               "error.implementation_error_cannot_show_view_alignment_frame"));
5471     }
5472     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5473             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5474     {
5475       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5476     }
5477   }
5478
5479   /**
5480    * Action on selection of menu options to Show or Hide annotations.
5481    *
5482    * @param visible
5483    * @param forSequences
5484    *          update sequence-related annotations
5485    * @param forAlignment
5486    *          update non-sequence-related annotations
5487    */
5488   @Override
5489   protected void setAnnotationsVisibility(boolean visible,
5490           boolean forSequences, boolean forAlignment)
5491   {
5492     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5493             .getAlignmentAnnotation();
5494     if (anns == null)
5495     {
5496       return;
5497     }
5498     for (AlignmentAnnotation aa : anns)
5499     {
5500       /*
5501        * don't display non-positional annotations on an alignment
5502        */
5503       if (aa.annotations == null)
5504       {
5505         continue;
5506       }
5507       boolean apply = (aa.sequenceRef == null && forAlignment)
5508               || (aa.sequenceRef != null && forSequences);
5509       if (apply)
5510       {
5511         aa.visible = visible;
5512       }
5513     }
5514     alignPanel.validateAnnotationDimensions(true);
5515     alignPanel.alignmentChanged();
5516   }
5517
5518   /**
5519    * Store selected annotation sort order for the view and repaint.
5520    */
5521   @Override
5522   protected void sortAnnotations_actionPerformed()
5523   {
5524     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5525     this.alignPanel.av
5526             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5527     alignPanel.paintAlignment(false, false);
5528   }
5529
5530   /**
5531    *
5532    * @return alignment panels in this alignment frame
5533    */
5534   public List<? extends AlignmentViewPanel> getAlignPanels()
5535   {
5536     // alignPanels is never null
5537     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5538     return alignPanels;
5539   }
5540
5541   /**
5542    * Open a new alignment window, with the cDNA associated with this (protein)
5543    * alignment, aligned as is the protein.
5544    */
5545   protected void viewAsCdna_actionPerformed()
5546   {
5547     // TODO no longer a menu action - refactor as required
5548     final AlignmentI alignment = getViewport().getAlignment();
5549     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5550     if (mappings == null)
5551     {
5552       return;
5553     }
5554     List<SequenceI> cdnaSeqs = new ArrayList<>();
5555     for (SequenceI aaSeq : alignment.getSequences())
5556     {
5557       for (AlignedCodonFrame acf : mappings)
5558       {
5559         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5560         if (dnaSeq != null)
5561         {
5562           /*
5563            * There is a cDNA mapping for this protein sequence - add to new
5564            * alignment. It will share the same dataset sequence as other mapped
5565            * cDNA (no new mappings need to be created).
5566            */
5567           final Sequence newSeq = new Sequence(dnaSeq);
5568           newSeq.setDatasetSequence(dnaSeq);
5569           cdnaSeqs.add(newSeq);
5570         }
5571       }
5572     }
5573     if (cdnaSeqs.size() == 0)
5574     {
5575       // show a warning dialog no mapped cDNA
5576       return;
5577     }
5578     AlignmentI cdna = new Alignment(
5579             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5580     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5581             AlignFrame.DEFAULT_HEIGHT);
5582     cdna.alignAs(alignment);
5583     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5584             + this.title;
5585     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5586             AlignFrame.DEFAULT_HEIGHT);
5587   }
5588
5589   /**
5590    * Set visibility of dna/protein complement view (available when shown in a
5591    * split frame).
5592    *
5593    * @param show
5594    */
5595   @Override
5596   protected void showComplement_actionPerformed(boolean show)
5597   {
5598     SplitContainerI sf = getSplitViewContainer();
5599     if (sf != null)
5600     {
5601       sf.setComplementVisible(this, show);
5602     }
5603   }
5604
5605   /**
5606    * Generate the reverse (optionally complemented) of the selected sequences,
5607    * and add them to the alignment
5608    */
5609   @Override
5610   protected void showReverse_actionPerformed(boolean complement)
5611   {
5612     AlignmentI al = null;
5613     try
5614     {
5615       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5616       al = dna.reverseCdna(complement);
5617       viewport.addAlignment(al, "");
5618       addHistoryItem(new EditCommand(
5619               MessageManager.getString("label.add_sequences"), Action.PASTE,
5620               al.getSequencesArray(), 0, al.getWidth(),
5621               viewport.getAlignment()));
5622     } catch (Exception ex)
5623     {
5624       System.err.println(ex.getMessage());
5625       return;
5626     }
5627   }
5628
5629   /**
5630    * Try to run a script in the Groovy console, having first ensured that this
5631    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5632    * be targeted at this alignment.
5633    */
5634   @Override
5635   protected void runGroovy_actionPerformed()
5636   {
5637     Jalview.setCurrentAlignFrame(this);
5638     groovy.ui.Console console = Desktop.getGroovyConsole();
5639     if (console != null)
5640     {
5641       try
5642       {
5643         console.runScript();
5644       } catch (Exception ex)
5645       {
5646         System.err.println((ex.toString()));
5647         JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
5648                 MessageManager.getString("label.couldnt_run_groovy_script"),
5649                 MessageManager.getString("label.groovy_support_failed"),
5650                 JvOptionPane.ERROR_MESSAGE);
5651       }
5652     }
5653     else
5654     {
5655       System.err.println("Can't run Groovy script as console not found");
5656     }
5657   }
5658
5659   /**
5660    * Hides columns containing (or not containing) a specified feature, provided
5661    * that would not leave all columns hidden
5662    *
5663    * @param featureType
5664    * @param columnsContaining
5665    * @return
5666    */
5667   public boolean hideFeatureColumns(String featureType,
5668           boolean columnsContaining)
5669   {
5670     boolean notForHiding = avc.markColumnsContainingFeatures(
5671             columnsContaining, false, false, featureType);
5672     if (notForHiding)
5673     {
5674       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5675               false, featureType))
5676       {
5677         getViewport().hideSelectedColumns();
5678         return true;
5679       }
5680     }
5681     return false;
5682   }
5683
5684   @Override
5685   protected void selectHighlightedColumns_actionPerformed(
5686           ActionEvent actionEvent)
5687   {
5688     // include key modifier check in case user selects from menu
5689     avc.markHighlightedColumns(
5690             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5691             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5692                     | ActionEvent.CTRL_MASK)) != 0);
5693   }
5694
5695   /**
5696    * Rebuilds the Colour menu, including any user-defined colours which have
5697    * been loaded either on startup or during the session
5698    */
5699   public void buildColourMenu()
5700   {
5701     colourMenu.removeAll();
5702
5703     colourMenu.add(applyToAllGroups);
5704     colourMenu.add(textColour);
5705     colourMenu.addSeparator();
5706
5707     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5708             viewport.getAlignment(), false);
5709
5710     colourMenu.add(annotationColour);
5711     bg.add(annotationColour);
5712     colourMenu.addSeparator();
5713     colourMenu.add(conservationMenuItem);
5714     colourMenu.add(modifyConservation);
5715     colourMenu.add(abovePIDThreshold);
5716     colourMenu.add(modifyPID);
5717
5718     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5719     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5720   }
5721
5722   /**
5723    * Open a dialog (if not already open) that allows the user to select and
5724    * calculate PCA or Tree analysis
5725    */
5726   protected void openTreePcaDialog()
5727   {
5728     if (alignPanel.getCalculationDialog() == null)
5729     {
5730       new CalculationChooser(AlignFrame.this);
5731     }
5732   }
5733
5734   @Override
5735   protected void loadVcf_actionPerformed()
5736   {
5737     JalviewFileChooser chooser = new JalviewFileChooser(
5738             Cache.getProperty("LAST_DIRECTORY"));
5739     chooser.setFileView(new JalviewFileView());
5740     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5741     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5742     final AlignFrame us = this;
5743     chooser.setResponseHandler(0, new Runnable()
5744     {
5745       @Override
5746       public void run()
5747       {
5748         String choice = chooser.getSelectedFile().getPath();
5749         Cache.setProperty("LAST_DIRECTORY", choice);
5750         SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5751         new VCFLoader(choice).loadVCF(seqs, us);
5752       }
5753     });
5754     chooser.showOpenDialog(null);
5755
5756   }
5757
5758 }
5759
5760 class PrintThread extends Thread
5761 {
5762   AlignmentPanel ap;
5763
5764   public PrintThread(AlignmentPanel ap)
5765   {
5766     this.ap = ap;
5767   }
5768
5769   static PageFormat pf;
5770
5771   @Override
5772   public void run()
5773   {
5774     PrinterJob printJob = PrinterJob.getPrinterJob();
5775
5776     if (pf != null)
5777     {
5778       printJob.setPrintable(ap, pf);
5779     }
5780     else
5781     {
5782       printJob.setPrintable(ap);
5783     }
5784
5785     if (printJob.printDialog())
5786     {
5787       try
5788       {
5789         printJob.print();
5790       } catch (Exception PrintException)
5791       {
5792         PrintException.printStackTrace();
5793       }
5794     }
5795   }
5796 }