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.Jalview;
  41 import jalview.commands.CommandI;
  42 import jalview.commands.EditCommand;
  43 import jalview.commands.EditCommand.Action;
  44 import jalview.commands.OrderCommand;
  45 import jalview.commands.RemoveGapColCommand;
  46 import jalview.commands.RemoveGapsCommand;
  47 import jalview.commands.SlideSequencesCommand;
  48 import jalview.commands.TrimRegionCommand;
  49 import jalview.datamodel.AlignExportSettingsAdapter;
  50 import jalview.datamodel.AlignedCodonFrame;
  51 import jalview.datamodel.Alignment;
  52 import jalview.datamodel.AlignmentAnnotation;
  53 import jalview.datamodel.AlignmentExportData;
  54 import jalview.datamodel.AlignmentI;
  55 import jalview.datamodel.AlignmentOrder;
  56 import jalview.datamodel.AlignmentView;
  57 import jalview.datamodel.ColumnSelection;
  58 import jalview.datamodel.HiddenColumns;
  59 import jalview.datamodel.PDBEntry;
  60 import jalview.datamodel.SeqCigar;
  61 import jalview.datamodel.Sequence;
  62 import jalview.datamodel.SequenceGroup;
  63 import jalview.datamodel.SequenceI;
  64 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  65 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  66 import jalview.io.AlignmentProperties;
  67 import jalview.io.AnnotationFile;
  68 import jalview.io.BackupFiles;
  69 import jalview.io.BioJsHTMLOutput;
  70 import jalview.io.DataSourceType;
  71 import jalview.io.FileFormat;
  72 import jalview.io.FileFormatI;
  73 import jalview.io.FileFormats;
  74 import jalview.io.FileLoader;
  75 import jalview.io.FileParse;
  76 import jalview.io.FormatAdapter;
  77 import jalview.io.HtmlSvgOutput;
  78 import jalview.io.IdentifyFile;
  79 import jalview.io.JPredFile;
  80 import jalview.io.JalviewFileChooser;
  81 import jalview.io.JalviewFileView;
  82 import jalview.io.JnetAnnotationMaker;
  83 import jalview.io.NewickFile;
  84 import jalview.io.ScoreMatrixFile;
  85 import jalview.io.TCoffeeScoreFile;
  86 import jalview.io.vcf.VCFLoader;
  87 import jalview.jbgui.GAlignFrame;
  88 import jalview.project.Jalview2XML;
  89 import jalview.schemes.ColourSchemeI;
  90 import jalview.schemes.ColourSchemes;
  91 import jalview.schemes.ResidueColourScheme;
  92 import jalview.schemes.TCoffeeColourScheme;
  93 import jalview.util.ImageMaker.TYPE;
  94 import jalview.util.MessageManager;
  95 import jalview.util.Platform;
  96 import jalview.viewmodel.AlignmentViewport;
  97 import jalview.viewmodel.ViewportRanges;
  98 import jalview.ws.DBRefFetcher;
  99 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 100 import jalview.ws.jws1.Discoverer;
 101 import jalview.ws.jws2.Jws2Discoverer;
 102 import jalview.ws.jws2.jabaws2.Jws2Instance;
 103 import jalview.ws.seqfetcher.DbSourceProxy;
 104
 105 import java.awt.BorderLayout;
 106 import java.awt.Color;
 107 import java.awt.Component;
 108 import java.awt.Rectangle;
 109 import java.awt.Toolkit;
 110 import java.awt.datatransfer.Clipboard;
 111 import java.awt.datatransfer.DataFlavor;
 112 import java.awt.datatransfer.StringSelection;
 113 import java.awt.datatransfer.Transferable;
 114 import java.awt.dnd.DnDConstants;
 115 import java.awt.dnd.DropTargetDragEvent;
 116 import java.awt.dnd.DropTargetDropEvent;
 117 import java.awt.dnd.DropTargetEvent;
 118 import java.awt.dnd.DropTargetListener;
 119 import java.awt.event.ActionEvent;
 120 import java.awt.event.ActionListener;
 121 import java.awt.event.FocusAdapter;
 122 import java.awt.event.FocusEvent;
 123 import java.awt.event.ItemEvent;
 124 import java.awt.event.ItemListener;
 125 import java.awt.event.KeyAdapter;
 126 import java.awt.event.KeyEvent;
 127 import java.awt.event.MouseEvent;
 128 import java.awt.print.PageFormat;
 129 import java.awt.print.PrinterJob;
 130 import java.beans.PropertyChangeEvent;
 131 import java.io.File;
 132 import java.io.FileWriter;
 133 import java.io.PrintWriter;
 134 import java.net.URL;
 135 import java.util.ArrayList;
 136 import java.util.Arrays;
 137 import java.util.Deque;
 138 import java.util.Enumeration;
 139 import java.util.Hashtable;
 140 import java.util.List;
 141 import java.util.Vector;
 142
 143 import javax.swing.ButtonGroup;
 144 import javax.swing.JCheckBoxMenuItem;
 145 import javax.swing.JComponent;
 146 import javax.swing.JEditorPane;
 147 import javax.swing.JInternalFrame;
 148 import javax.swing.JLabel;
 149 import javax.swing.JLayeredPane;
 150 import javax.swing.JMenu;
 151 import javax.swing.JMenuItem;
 152 import javax.swing.JPanel;
 153 import javax.swing.JScrollPane;
 154 import javax.swing.SwingUtilities;
 155
 156 /**
 157  * DOCUMENT ME!
 158  *
 159  * @author $author$
 160  * @version $Revision$
 161  */
 162 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 163         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 164 {
 165
 166   public static final int DEFAULT_WIDTH = 700;
 167
 168   public static final int DEFAULT_HEIGHT = 500;
 169
 170   /*
 171    * The currently displayed panel (selected tabbed view if more than one)
 172    */
 173   public AlignmentPanel alignPanel;
 174
 175   AlignViewport viewport;
 176
 177   public AlignViewControllerI avc;
 178
 179   List<AlignmentPanel> alignPanels = new ArrayList<>();
 180
 181   /**
 182    * Last format used to load or save alignments in this window
 183    */
 184   FileFormatI currentFileFormat = null;
 185
 186   /**
 187    * Current filename for this alignment
 188    */
 189   String fileName = null;
 190
 191   File fileObject;
 192
 193   /**
 194    * Creates a new AlignFrame object with specific width and height.
 195    *
 196    * @param al
 197    * @param width
 198    * @param height
 199    */
 200   public AlignFrame(AlignmentI al, int width, int height)
 201   {
 202     this(al, null, width, height);
 203   }
 204
 205   /**
 206    * Creates a new AlignFrame object with specific width, height and
 207    * sequenceSetId
 208    *
 209    * @param al
 210    * @param width
 211    * @param height
 212    * @param sequenceSetId
 213    */
 214   public AlignFrame(AlignmentI al, int width, int height,
 215           String sequenceSetId)
 216   {
 217     this(al, null, width, height, sequenceSetId);
 218   }
 219
 220   /**
 221    * Creates a new AlignFrame object with specific width, height and
 222    * sequenceSetId
 223    *
 224    * @param al
 225    * @param width
 226    * @param height
 227    * @param sequenceSetId
 228    * @param viewId
 229    */
 230   public AlignFrame(AlignmentI al, int width, int height,
 231           String sequenceSetId, String viewId)
 232   {
 233     this(al, null, width, height, sequenceSetId, viewId);
 234   }
 235
 236   /**
 237    * new alignment window with hidden columns
 238    *
 239    * @param al
 240    *          AlignmentI
 241    * @param hiddenColumns
 242    *          ColumnSelection or null
 243    * @param width
 244    *          Width of alignment frame
 245    * @param height
 246    *          height of frame.
 247    */
 248   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 249           int height)
 250   {
 251     this(al, hiddenColumns, width, height, null);
 252   }
 253
 254   /**
 255    * Create alignment frame for al with hiddenColumns, a specific width and
 256    * height, and specific sequenceId
 257    *
 258    * @param al
 259    * @param hiddenColumns
 260    * @param width
 261    * @param height
 262    * @param sequenceSetId
 263    *          (may be null)
 264    */
 265   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 266           int height, String sequenceSetId)
 267   {
 268     this(al, hiddenColumns, width, height, sequenceSetId, null);
 269   }
 270
 271   /**
 272    * Create alignment frame for al with hiddenColumns, a specific width and
 273    * height, and specific sequenceId
 274    *
 275    * @param al
 276    * @param hiddenColumns
 277    * @param width
 278    * @param height
 279    * @param sequenceSetId
 280    *          (may be null)
 281    * @param viewId
 282    *          (may be null)
 283    */
 284   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 285           int height, String sequenceSetId, String viewId)
 286   {
 287     setSize(width, height);
 288
 289     if (al.getDataset() == null)
 290     {
 291       al.setDataset(null);
 292     }
 293
 294     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 295
 296     alignPanel = new AlignmentPanel(this, viewport);
 297
 298     addAlignmentPanel(alignPanel, true);
 299     init();
 300   }
 301
 302   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 303           HiddenColumns hiddenColumns, int width, int height)
 304   {
 305     setSize(width, height);
 306
 307     if (al.getDataset() == null)
 308     {
 309       al.setDataset(null);
 310     }
 311
 312     viewport = new AlignViewport(al, hiddenColumns);
 313
 314     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 315     {
 316       viewport.hideSequence(hiddenSeqs);
 317     }
 318     alignPanel = new AlignmentPanel(this, viewport);
 319     addAlignmentPanel(alignPanel, true);
 320     init();
 321   }
 322
 323   /**
 324    * Make a new AlignFrame from existing alignmentPanels
 325    *
 326    * @param ap
 327    *          AlignmentPanel
 328    * @param av
 329    *          AlignViewport
 330    */
 331   public AlignFrame(AlignmentPanel ap)
 332   {
 333     viewport = ap.av;
 334     alignPanel = ap;
 335     addAlignmentPanel(ap, false);
 336     init();
 337   }
 338
 339   /**
 340    * initalise the alignframe from the underlying viewport data and the
 341    * configurations
 342    */
 343   void init()
 344   {
 345 //        setBackground(Color.white); // BH 2019
 346
 347     if (!Jalview.isHeadlessMode())
 348     {
 349       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 350     }
 351
 352     avc = new jalview.controller.AlignViewController(this, viewport,
 353             alignPanel);
 354     if (viewport.getAlignmentConservationAnnotation() == null)
 355     {
 356       // BLOSUM62Colour.setEnabled(false);
 357       conservationMenuItem.setEnabled(false);
 358       modifyConservation.setEnabled(false);
 359       // PIDColour.setEnabled(false);
 360       // abovePIDThreshold.setEnabled(false);
 361       // modifyPID.setEnabled(false);
 362     }
 363
 364     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 365             "No sort");
 366
 367     if (sortby.equals("Id"))
 368     {
 369       sortIDMenuItem_actionPerformed(null);
 370     }
 371     else if (sortby.equals("Pairwise Identity"))
 372     {
 373       sortPairwiseMenuItem_actionPerformed(null);
 374     }
 375
 376     this.alignPanel.av
 377             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 378
 379     setMenusFromViewport(viewport);
 380     buildSortByAnnotationScoresMenu();
 381     calculateTree.addActionListener(new ActionListener()
 382     {
 383
 384       @Override
 385       public void actionPerformed(ActionEvent e)
 386       {
 387         openTreePcaDialog();
 388       }
 389     });
 390     buildColourMenu();
 391
 392     if (Desktop.desktop != null)
 393     {
 394       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 395       /**
 396        * BH 2018 ignore service listeners
 397        *
 398        * @j2sNative
 399        *
 400        */
 401       {
 402         addServiceListeners();
 403       }
 404       setGUINucleotide();
 405     }
 406
 407     if (viewport.getWrapAlignment())
 408     {
 409       wrapMenuItem_actionPerformed(null);
 410     }
 411
 412     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 413     {
 414       this.overviewMenuItem_actionPerformed(null);
 415     }
 416
 417     addKeyListener();
 418
 419     final List<AlignmentPanel> selviews = new ArrayList<>();
 420     final List<AlignmentPanel> origview = new ArrayList<>();
 421     final String menuLabel = MessageManager
 422             .getString("label.copy_format_from");
 423     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 424             new ViewSetProvider()
 425             {
 426
 427               @Override
 428               public AlignmentPanel[] getAllAlignmentPanels()
 429               {
 430                 origview.clear();
 431                 origview.add(alignPanel);
 432                 // make an array of all alignment panels except for this one
 433                 List<AlignmentPanel> aps = new ArrayList<>(
 434                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 435                 aps.remove(AlignFrame.this.alignPanel);
 436                 return aps.toArray(new AlignmentPanel[aps.size()]);
 437               }
 438             }, selviews, new ItemListener()
 439             {
 440
 441               @Override
 442               public void itemStateChanged(ItemEvent e)
 443               {
 444                 if (origview.size() > 0)
 445                 {
 446                   final AlignmentPanel ap = origview.get(0);
 447
 448                   /*
 449                    * Copy the ViewStyle of the selected panel to 'this one'.
 450                    * Don't change value of 'scaleProteinAsCdna' unless copying
 451                    * from a SplitFrame.
 452                    */
 453                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 454                           .getViewStyle();
 455                   boolean fromSplitFrame = selviews.get(0)
 456                           .getAlignViewport().getCodingComplement() != null;
 457                   if (!fromSplitFrame)
 458                   {
 459                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 460                             .getViewStyle().isScaleProteinAsCdna());
 461                   }
 462                   ap.getAlignViewport().setViewStyle(vs);
 463
 464                   /*
 465                    * Also rescale ViewStyle of SplitFrame complement if there is
 466                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 467                    * the whole ViewStyle (allow cDNA protein to have different
 468                    * fonts)
 469                    */
 470                   AlignViewportI complement = ap.getAlignViewport()
 471                           .getCodingComplement();
 472                   if (complement != null && vs.isScaleProteinAsCdna())
 473                   {
 474                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 475                     ((SplitFrame) af.getSplitViewContainer())
 476                             .adjustLayout();
 477                     af.setMenusForViewport();
 478                   }
 479
 480                   ap.updateLayout();
 481                   ap.setSelected(true);
 482                   ap.alignFrame.setMenusForViewport();
 483
 484                 }
 485               }
 486             });
 487     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 488             .indexOf("devel") > -1
 489             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 490                     .indexOf("test") > -1)
 491     {
 492       formatMenu.add(vsel);
 493     }
 494     addFocusListener(new FocusAdapter()
 495     {
 496       @Override
 497       public void focusGained(FocusEvent e)
 498       {
 499         Jalview.setCurrentAlignFrame(AlignFrame.this);
 500       }
 501     });
 502
 503   }
 504
 505   /**
 506    * Change the filename and format for the alignment, and enable the 'reload'
 507    * button functionality.
 508    *
 509    * @param file
 510    *          valid filename
 511    * @param format
 512    *          format of file
 513    */
 514   public void setFileName(String file, FileFormatI format)
 515   {
 516     fileName = file;
 517     setFileFormat(format);
 518     reload.setEnabled(true);
 519   }
 520
 521   /**
 522    * JavaScript will have this, maybe others. More dependable than a file name
 523    * and maintains a reference to the actual bytes loaded.
 524    *
 525    * @param file
 526    */
 527   public void setFileObject(File file)
 528   {
 529     this.fileObject = file;
 530   }
 531
 532   /**
 533    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 534    * events
 535    */
 536   void addKeyListener()
 537   {
 538     addKeyListener(new KeyAdapter()
 539     {
 540       @Override
 541       public void keyPressed(KeyEvent evt)
 542       {
 543         if (viewport.cursorMode
 544                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 545                         && evt.getKeyCode() <= KeyEvent.VK_9)
 546                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 547                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 548                 && Character.isDigit(evt.getKeyChar()))
 549         {
 550           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 551         }
 552
 553         switch (evt.getKeyCode())
 554         {
 555
 556         case 27: // escape key
 557           deselectAllSequenceMenuItem_actionPerformed(null);
 558
 559           break;
 560
 561         case KeyEvent.VK_DOWN:
 562           if (evt.isAltDown() || !viewport.cursorMode)
 563           {
 564             moveSelectedSequences(false);
 565           }
 566           if (viewport.cursorMode)
 567           {
 568             alignPanel.getSeqPanel().moveCursor(0, 1);
 569           }
 570           break;
 571
 572         case KeyEvent.VK_UP:
 573           if (evt.isAltDown() || !viewport.cursorMode)
 574           {
 575             moveSelectedSequences(true);
 576           }
 577           if (viewport.cursorMode)
 578           {
 579             alignPanel.getSeqPanel().moveCursor(0, -1);
 580           }
 581
 582           break;
 583
 584         case KeyEvent.VK_LEFT:
 585           if (evt.isAltDown() || !viewport.cursorMode)
 586           {
 587             slideSequences(false,
 588                     alignPanel.getSeqPanel().getKeyboardNo1());
 589           }
 590           else
 591           {
 592             alignPanel.getSeqPanel().moveCursor(-1, 0);
 593           }
 594
 595           break;
 596
 597         case KeyEvent.VK_RIGHT:
 598           if (evt.isAltDown() || !viewport.cursorMode)
 599           {
 600             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 601           }
 602           else
 603           {
 604             alignPanel.getSeqPanel().moveCursor(1, 0);
 605           }
 606           break;
 607
 608         case KeyEvent.VK_SPACE:
 609           if (viewport.cursorMode)
 610           {
 611             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 612                     || evt.isShiftDown() || evt.isAltDown());
 613           }
 614           break;
 615
 616         // case KeyEvent.VK_A:
 617         // if (viewport.cursorMode)
 618         // {
 619         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 620         // //System.out.println("A");
 621         // }
 622         // break;
 623         /*
 624          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 625          * System.out.println("closing bracket"); } break;
 626          */
 627         case KeyEvent.VK_DELETE:
 628         case KeyEvent.VK_BACK_SPACE:
 629           if (!viewport.cursorMode)
 630           {
 631             cut_actionPerformed();
 632           }
 633           else
 634           {
 635             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 636                     || evt.isShiftDown() || evt.isAltDown());
 637           }
 638
 639           break;
 640
 641         case KeyEvent.VK_S:
 642           if (viewport.cursorMode)
 643           {
 644             alignPanel.getSeqPanel().setCursorRow();
 645           }
 646           break;
 647         case KeyEvent.VK_C:
 648           if (viewport.cursorMode && !evt.isControlDown())
 649           {
 650             alignPanel.getSeqPanel().setCursorColumn();
 651           }
 652           break;
 653         case KeyEvent.VK_P:
 654           if (viewport.cursorMode)
 655           {
 656             alignPanel.getSeqPanel().setCursorPosition();
 657           }
 658           break;
 659
 660         case KeyEvent.VK_ENTER:
 661         case KeyEvent.VK_COMMA:
 662           if (viewport.cursorMode)
 663           {
 664             alignPanel.getSeqPanel().setCursorRowAndColumn();
 665           }
 666           break;
 667
 668         case KeyEvent.VK_Q:
 669           if (viewport.cursorMode)
 670           {
 671             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 672           }
 673           break;
 674         case KeyEvent.VK_M:
 675           if (viewport.cursorMode)
 676           {
 677             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 678           }
 679           break;
 680
 681         case KeyEvent.VK_F2:
 682           viewport.cursorMode = !viewport.cursorMode;
 683           setStatus(MessageManager
 684                   .formatMessage("label.keyboard_editing_mode", new String[]
 685                   { (viewport.cursorMode ? "on" : "off") }));
 686           if (viewport.cursorMode)
 687           {
 688             ViewportRanges ranges = viewport.getRanges();
 689             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 690                     .getStartRes();
 691             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 692                     .getStartSeq();
 693           }
 694           alignPanel.getSeqPanel().seqCanvas.repaint();
 695           break;
 696
 697         case KeyEvent.VK_F1:
 698           try
 699           {
 700             Help.showHelpWindow();
 701           } catch (Exception ex)
 702           {
 703             ex.printStackTrace();
 704           }
 705           break;
 706         case KeyEvent.VK_H:
 707         {
 708           boolean toggleSeqs = !evt.isControlDown();
 709           boolean toggleCols = !evt.isShiftDown();
 710           toggleHiddenRegions(toggleSeqs, toggleCols);
 711           break;
 712         }
 713         case KeyEvent.VK_B:
 714         {
 715           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 716           boolean modifyExisting = true; // always modify, don't clear
 717                                          // evt.isShiftDown();
 718           boolean invertHighlighted = evt.isAltDown();
 719           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 720                   toggleSel);
 721           break;
 722         }
 723         case KeyEvent.VK_PAGE_UP:
 724           viewport.getRanges().pageUp();
 725           break;
 726         case KeyEvent.VK_PAGE_DOWN:
 727           viewport.getRanges().pageDown();
 728           break;
 729         }
 730       }
 731
 732       @Override
 733       public void keyReleased(KeyEvent evt)
 734       {
 735         switch (evt.getKeyCode())
 736         {
 737         case KeyEvent.VK_LEFT:
 738           if (evt.isAltDown() || !viewport.cursorMode)
 739           {
 740             viewport.firePropertyChange("alignment", null,
 741                     viewport.getAlignment().getSequences());
 742           }
 743           break;
 744
 745         case KeyEvent.VK_RIGHT:
 746           if (evt.isAltDown() || !viewport.cursorMode)
 747           {
 748             viewport.firePropertyChange("alignment", null,
 749                     viewport.getAlignment().getSequences());
 750           }
 751           break;
 752         }
 753       }
 754     });
 755   }
 756
 757   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 758   {
 759     ap.alignFrame = this;
 760     avc = new jalview.controller.AlignViewController(this, viewport,
 761             alignPanel);
 762
 763     alignPanels.add(ap);
 764
 765     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 766
 767     int aSize = alignPanels.size();
 768
 769     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 770
 771     if (aSize == 1 && ap.av.getViewName() == null)
 772     {
 773       this.getContentPane().add(ap, BorderLayout.CENTER);
 774     }
 775     else
 776     {
 777       if (aSize == 2)
 778       {
 779         setInitialTabVisible();
 780       }
 781
 782       expandViews.setEnabled(true);
 783       gatherViews.setEnabled(true);
 784       tabbedPane.addTab(ap.av.getViewName(), ap);
 785
 786       ap.setVisible(false);
 787     }
 788
 789     if (newPanel)
 790     {
 791       if (ap.av.isPadGaps())
 792       {
 793         ap.av.getAlignment().padGaps();
 794       }
 795       ap.av.updateConservation(ap);
 796       ap.av.updateConsensus(ap);
 797       ap.av.updateStrucConsensus(ap);
 798     }
 799   }
 800
 801   public void setInitialTabVisible()
 802   {
 803     expandViews.setEnabled(true);
 804     gatherViews.setEnabled(true);
 805     tabbedPane.setVisible(true);
 806     AlignmentPanel first = alignPanels.get(0);
 807     tabbedPane.addTab(first.av.getViewName(), first);
 808     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 809   }
 810
 811   public AlignViewport getViewport()
 812   {
 813     return viewport;
 814   }
 815
 816   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 817   private void addServiceListeners()
 818   {
 819     final java.beans.PropertyChangeListener thisListener;
 820     Desktop.instance.addJalviewPropertyChangeListener("services",
 821             thisListener = new java.beans.PropertyChangeListener()
 822             {
 823               @Override
 824               public void propertyChange(PropertyChangeEvent evt)
 825               {
 826                 // // System.out.println("Discoverer property change.");
 827                 // if (evt.getPropertyName().equals("services"))
 828                 {
 829                   SwingUtilities.invokeLater(new Runnable()
 830                   {
 831
 832                     @Override
 833                     public void run()
 834                     {
 835                       System.err.println(
 836                               "Rebuild WS Menu for service change");
 837                       BuildWebServiceMenu();
 838                     }
 839
 840                   });
 841                 }
 842               }
 843             });
 844     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 845     {
 846       @Override
 847       public void internalFrameClosed(
 848               javax.swing.event.InternalFrameEvent evt)
 849       {
 850         // System.out.println("deregistering discoverer listener");
 851         Desktop.instance.removeJalviewPropertyChangeListener("services",
 852                 thisListener);
 853         closeMenuItem_actionPerformed(true);
 854       }
 855     });
 856     // Finally, build the menu once to get current service state
 857     new Thread(new Runnable()
 858     {
 859       @Override
 860       public void run()
 861       {
 862         BuildWebServiceMenu();
 863       }
 864     }).start();
 865   }
 866
 867   /**
 868    * Configure menu items that vary according to whether the alignment is
 869    * nucleotide or protein
 870    */
 871   public void setGUINucleotide()
 872   {
 873     AlignmentI al = getViewport().getAlignment();
 874     boolean nucleotide = al.isNucleotide();
 875
 876     loadVcf.setVisible(nucleotide);
 877     showTranslation.setVisible(nucleotide);
 878     showReverse.setVisible(nucleotide);
 879     showReverseComplement.setVisible(nucleotide);
 880     conservationMenuItem.setEnabled(!nucleotide);
 881     modifyConservation
 882             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 883     showGroupConservation.setEnabled(!nucleotide);
 884
 885     showComplementMenuItem
 886             .setText(nucleotide ? MessageManager.getString("label.protein")
 887                     : MessageManager.getString("label.nucleotide"));
 888   }
 889
 890   /**
 891    * set up menus for the current viewport. This may be called after any
 892    * operation that affects the data in the current view (selection changed,
 893    * etc) to update the menus to reflect the new state.
 894    */
 895   @Override
 896   public void setMenusForViewport()
 897   {
 898     setMenusFromViewport(viewport);
 899   }
 900
 901   /**
 902    * Need to call this method when tabs are selected for multiple views, or when
 903    * loading from Jalview2XML.java
 904    *
 905    * @param av
 906    *          AlignViewport
 907    */
 908   public void setMenusFromViewport(AlignViewport av)
 909   {
 910     padGapsMenuitem.setSelected(av.isPadGaps());
 911     colourTextMenuItem.setSelected(av.isShowColourText());
 912     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 913     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 914     conservationMenuItem.setSelected(av.getConservationSelected());
 915     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 916     seqLimits.setSelected(av.getShowJVSuffix());
 917     idRightAlign.setSelected(av.isRightAlignIds());
 918     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 919     renderGapsMenuItem.setSelected(av.isRenderGaps());
 920     wrapMenuItem.setSelected(av.getWrapAlignment());
 921     scaleAbove.setVisible(av.getWrapAlignment());
 922     scaleLeft.setVisible(av.getWrapAlignment());
 923     scaleRight.setVisible(av.getWrapAlignment());
 924     annotationPanelMenuItem.setState(av.isShowAnnotation());
 925     /*
 926      * Show/hide annotations only enabled if annotation panel is shown
 927      */
 928     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 929     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 930     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 931     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 932     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 933     viewTextMenuItem.setSelected(av.getShowText());
 934     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 935     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 936     showGroupConservation.setSelected(av.isShowGroupConservation());
 937     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 938     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 939     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 940
 941     ColourMenuHelper.setColourSelected(colourMenu,
 942             av.getGlobalColourScheme());
 943
 944     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 945     hiddenMarkers.setState(av.getShowHiddenMarkers());
 946     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 947     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 948     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 949     autoCalculate.setSelected(av.autoCalculateConsensus);
 950     sortByTree.setSelected(av.sortByTree);
 951     listenToViewSelections.setSelected(av.followSelection);
 952
 953     showProducts.setEnabled(canShowProducts());
 954     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 955
 956     updateEditMenuBar();
 957   }
 958
 959   /**
 960    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 961    *
 962    * @param b
 963    */
 964   public void setGroovyEnabled(boolean b)
 965   {
 966     runGroovy.setEnabled(b);
 967   }
 968
 969   private IProgressIndicator progressBar;
 970
 971   /*
 972    * (non-Javadoc)
 973    *
 974    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 975    */
 976   @Override
 977   public void setProgressBar(String message, long id)
 978   {
 979     progressBar.setProgressBar(message, id);
 980   }
 981
 982   @Override
 983   public void registerHandler(final long id,
 984           final IProgressIndicatorHandler handler)
 985   {
 986     progressBar.registerHandler(id, handler);
 987   }
 988
 989   /**
 990    *
 991    * @return true if any progress bars are still active
 992    */
 993   @Override
 994   public boolean operationInProgress()
 995   {
 996     return progressBar.operationInProgress();
 997   }
 998
 999   /**
1000    * Sets the text of the status bar. Note that setting a null or empty value
1001    * will cause the status bar to be hidden, with possibly undesirable flicker
1002    * of the screen layout.
1003    */
1004   @Override
1005   public void setStatus(String text)
1006   {
1007     statusBar.setText(text == null || text.isEmpty() ? " " : text);
1008   }
1009
1010   /*
1011    * Added so Castor Mapping file can obtain Jalview Version
1012    */
1013   public String getVersion()
1014   {
1015     return jalview.bin.Cache.getProperty("VERSION");
1016   }
1017
1018   public FeatureRenderer getFeatureRenderer()
1019   {
1020     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1021   }
1022
1023   @Override
1024   public void fetchSequence_actionPerformed()
1025   {
1026     new SequenceFetcher(this);
1027   }
1028
1029   @Override
1030   public void addFromFile_actionPerformed(ActionEvent e)
1031   {
1032     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1033   }
1034
1035   @Override
1036   public void reload_actionPerformed(ActionEvent e)
1037   {
1038     if (fileName != null)
1039     {
1040       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1041       // originating file's format
1042       // TODO: work out how to recover feature settings for correct view(s) when
1043       // file is reloaded.
1044       if (FileFormat.Jalview.equals(currentFileFormat))
1045       {
1046         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1047         for (int i = 0; i < frames.length; i++)
1048         {
1049           if (frames[i] instanceof AlignFrame && frames[i] != this
1050                   && ((AlignFrame) frames[i]).fileName != null
1051                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1052           {
1053             try
1054             {
1055               frames[i].setSelected(true);
1056               Desktop.instance.closeAssociatedWindows();
1057             } catch (java.beans.PropertyVetoException ex)
1058             {
1059             }
1060           }
1061
1062         }
1063         Desktop.instance.closeAssociatedWindows();
1064
1065         FileLoader loader = new FileLoader();
1066         DataSourceType protocol = fileName.startsWith("http:")
1067                 ? DataSourceType.URL
1068                 : DataSourceType.FILE;
1069         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1070       }
1071       else
1072       {
1073         Rectangle bounds = this.getBounds();
1074
1075         FileLoader loader = new FileLoader();
1076
1077         AlignFrame newframe = null;
1078
1079         if (fileObject == null)
1080         {
1081
1082           DataSourceType protocol = (fileName.startsWith("http:")
1083                   ? DataSourceType.URL
1084                   : DataSourceType.FILE);
1085           newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1086                   currentFileFormat);
1087         }
1088         else
1089         {
1090           newframe = loader.LoadFileWaitTillLoaded(fileObject,
1091                   DataSourceType.FILE, currentFileFormat);
1092         }
1093
1094         newframe.setBounds(bounds);
1095         if (featureSettings != null && featureSettings.isShowing())
1096         {
1097           final Rectangle fspos = featureSettings.frame.getBounds();
1098           // TODO: need a 'show feature settings' function that takes bounds -
1099           // need to refactor Desktop.addFrame
1100           newframe.featureSettings_actionPerformed(null);
1101           final FeatureSettings nfs = newframe.featureSettings;
1102           SwingUtilities.invokeLater(new Runnable()
1103           {
1104             @Override
1105             public void run()
1106             {
1107               nfs.frame.setBounds(fspos);
1108             }
1109           });
1110           this.featureSettings.close();
1111           this.featureSettings = null;
1112         }
1113         this.closeMenuItem_actionPerformed(true);
1114       }
1115     }
1116   }
1117
1118   @Override
1119   public void addFromText_actionPerformed(ActionEvent e)
1120   {
1121     Desktop.instance
1122             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1123   }
1124
1125   @Override
1126   public void addFromURL_actionPerformed(ActionEvent e)
1127   {
1128     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1129   }
1130
1131   @Override
1132   public void save_actionPerformed(ActionEvent e)
1133   {
1134     if (fileName == null || (currentFileFormat == null)
1135             || fileName.startsWith("http"))
1136     {
1137       saveAs_actionPerformed();
1138     }
1139     else
1140     {
1141       saveAlignment(fileName, currentFileFormat);
1142     }
1143   }
1144
1145   /**
1146    * Saves the alignment to a file with a name chosen by the user, if necessary
1147    * warning if a file would be overwritten
1148    */
1149   @Override
1150   public void saveAs_actionPerformed()
1151   {
1152     String format = currentFileFormat == null ? null
1153             : currentFileFormat.getName();
1154     JalviewFileChooser chooser = JalviewFileChooser
1155             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1156
1157     chooser.setFileView(new JalviewFileView());
1158     chooser.setDialogTitle(
1159             MessageManager.getString("label.save_alignment_to_file"));
1160     chooser.setToolTipText(MessageManager.getString("action.save"));
1161
1162     int value = chooser.showSaveDialog(this);
1163
1164     if (value != JalviewFileChooser.APPROVE_OPTION)
1165     {
1166       return;
1167     }
1168     currentFileFormat = chooser.getSelectedFormat();
1169     // todo is this (2005) test now obsolete - value is never null?
1170     while (currentFileFormat == null)
1171     {
1172       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1173               MessageManager
1174                       .getString("label.select_file_format_before_saving"),
1175               MessageManager.getString("label.file_format_not_specified"),
1176               JvOptionPane.WARNING_MESSAGE);
1177       currentFileFormat = chooser.getSelectedFormat();
1178       value = chooser.showSaveDialog(this);
1179       if (value != JalviewFileChooser.APPROVE_OPTION)
1180       {
1181         return;
1182       }
1183     }
1184
1185     fileName = chooser.getSelectedFile().getPath();
1186
1187     Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1188     Cache.setProperty("LAST_DIRECTORY", fileName);
1189     saveAlignment(fileName, currentFileFormat);
1190   }
1191
1192   boolean lastSaveSuccessful = false;
1193
1194   FileFormatI lastFormatSaved;
1195
1196   String lastFilenameSaved;
1197
1198   /**
1199    * Raise a dialog or status message for the last call to saveAlignment.
1200    *
1201    * @return true if last call to saveAlignment(file, format) was successful.
1202    */
1203   public boolean isSaveAlignmentSuccessful()
1204   {
1205
1206     if (!lastSaveSuccessful)
1207     {
1208       JvOptionPane.showInternalMessageDialog(this, MessageManager
1209               .formatMessage("label.couldnt_save_file", new Object[]
1210               { lastFilenameSaved }),
1211               MessageManager.getString("label.error_saving_file"),
1212               JvOptionPane.WARNING_MESSAGE);
1213     }
1214     else
1215     {
1216
1217       setStatus(MessageManager.formatMessage(
1218               "label.successfully_saved_to_file_in_format", new Object[]
1219               { lastFilenameSaved, lastFormatSaved }));
1220
1221     }
1222     return lastSaveSuccessful;
1223   }
1224
1225   /**
1226    * Saves the alignment to the specified file path, in the specified format,
1227    * which may be an alignment format, or Jalview project format. If the
1228    * alignment has hidden regions, or the format is one capable of including
1229    * non-sequence data (features, annotations, groups), then the user may be
1230    * prompted to specify what to include in the output.
1231    *
1232    * @param file
1233    * @param format
1234    */
1235   public void saveAlignment(String file, FileFormatI format)
1236   {
1237     lastSaveSuccessful = true;
1238     lastFilenameSaved = file;
1239     lastFormatSaved = format;
1240
1241     if (FileFormat.Jalview.equals(format))
1242     {
1243       String shortName = title;
1244       if (shortName.indexOf(File.separatorChar) > -1)
1245       {
1246         shortName = shortName.substring(
1247                 shortName.lastIndexOf(File.separatorChar) + 1);
1248       }
1249       lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName);
1250
1251       statusBar.setText(MessageManager.formatMessage(
1252               "label.successfully_saved_to_file_in_format", new Object[]
1253               { fileName, format }));
1254
1255       return;
1256     }
1257
1258     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1259     Runnable cancelAction = new Runnable()
1260     {
1261       @Override
1262       public void run()
1263       {
1264         lastSaveSuccessful = false;
1265       }
1266     };
1267     Runnable outputAction = new Runnable()
1268     {
1269       @Override
1270       public void run()
1271       {
1272         // todo defer this to inside formatSequences (or later)
1273         AlignmentExportData exportData = viewport
1274                 .getAlignExportData(options);
1275         String output = new FormatAdapter(alignPanel, options)
1276                 .formatSequences(format, exportData.getAlignment(),
1277                         exportData.getOmitHidden(),
1278                         exportData.getStartEndPostions(),
1279                         viewport.getAlignment().getHiddenColumns());
1280         if (output == null)
1281         {
1282           lastSaveSuccessful = false;
1283         }
1284         else
1285         {
1286           // create backupfiles object and get new temp filename destination
1287           boolean doBackup = BackupFiles.getEnabled();
1288           BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
1289           try
1290           {
1291             String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
1292                         PrintWriter out = new PrintWriter(
1293                     new FileWriter(tempFilePath));
1294
1295             out.print(output);
1296             out.close();
1297             AlignFrame.this.setTitle(file);
1298             statusBar.setText(MessageManager.formatMessage(
1299                   "label.successfully_saved_to_file_in_format", new Object[]
1300                   { fileName, format.getName() }));
1301             lastSaveSuccessful = true;
1302           } catch (Exception ex)
1303           {
1304             lastSaveSuccessful = false;
1305             ex.printStackTrace();
1306           }
1307
1308           if (doBackup)
1309           {
1310             backupfiles.setWriteSuccess(lastSaveSuccessful);
1311             // do the backup file roll and rename the temp file to actual file
1312             lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
1313           }
1314         }
1315       }
1316     };
1317
1318     /*
1319      * show dialog with export options if applicable; else just do it
1320      */
1321     if (AlignExportOptions.isNeeded(viewport, format))
1322     {
1323       AlignExportOptions choices = new AlignExportOptions(
1324               alignPanel.getAlignViewport(), format, options);
1325       choices.setResponseAction(0, outputAction);
1326       choices.setResponseAction(1, cancelAction);
1327       choices.showDialog();
1328     }
1329     else
1330     {
1331       outputAction.run();
1332     }
1333   }
1334
1335   /**
1336    * Outputs the alignment to textbox in the requested format, if necessary
1337    * first prompting the user for whether to include hidden regions or
1338    * non-sequence data
1339    *
1340    * @param fileFormatName
1341    */
1342   @Override
1343   protected void outputText_actionPerformed(String fileFormatName)
1344   {
1345     FileFormatI fileFormat = FileFormats.getInstance()
1346             .forName(fileFormatName);
1347     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1348     Runnable outputAction = new Runnable()
1349     {
1350       @Override
1351       public void run()
1352       {
1353         // todo defer this to inside formatSequences (or later)
1354         AlignmentExportData exportData = viewport
1355                 .getAlignExportData(options);
1356         CutAndPasteTransfer cap = new CutAndPasteTransfer();
1357         cap.setForInput(null);
1358         try
1359         {
1360           FileFormatI format = fileFormat;
1361           cap.setText(new FormatAdapter(alignPanel, options)
1362                   .formatSequences(format, exportData.getAlignment(),
1363                           exportData.getOmitHidden(),
1364                           exportData.getStartEndPostions(),
1365                           viewport.getAlignment().getHiddenColumns()));
1366           Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1367                   "label.alignment_output_command", new Object[]
1368                   { fileFormat.getName() }), 600, 500);
1369         } catch (OutOfMemoryError oom)
1370         {
1371           new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1372                   oom);
1373           cap.dispose();
1374         }
1375       }
1376     };
1377
1378     /*
1379      * show dialog with export options if applicable; else just do it
1380      */
1381     if (AlignExportOptions.isNeeded(viewport, fileFormat))
1382     {
1383       AlignExportOptions choices = new AlignExportOptions(
1384               alignPanel.getAlignViewport(), fileFormat, options);
1385       choices.setResponseAction(0, outputAction);
1386       choices.showDialog();
1387     }
1388     else
1389     {
1390       outputAction.run();
1391     }
1392   }
1393
1394   /**
1395    * DOCUMENT ME!
1396    *
1397    * @param e
1398    *          DOCUMENT ME!
1399    */
1400   @Override
1401   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1402   {
1403     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1404     htmlSVG.exportHTML(null);
1405   }
1406
1407   @Override
1408   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1409   {
1410     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1411     bjs.exportHTML(null);
1412   }
1413
1414   public void createImageMap(File file, String image)
1415   {
1416     alignPanel.makePNGImageMap(file, image);
1417   }
1418
1419   /**
1420    * Creates a PNG image of the alignment and writes it to the given file. If
1421    * the file is null, the user is prompted to choose a file.
1422    *
1423    * @param f
1424    */
1425   @Override
1426   public void createPNG(File f)
1427   {
1428     alignPanel.makeAlignmentImage(TYPE.PNG, f);
1429   }
1430
1431   /**
1432    * Creates an EPS image of the alignment and writes it to the given file. If
1433    * the file is null, the user is prompted to choose a file.
1434    *
1435    * @param f
1436    */
1437   @Override
1438   public void createEPS(File f)
1439   {
1440     alignPanel.makeAlignmentImage(TYPE.EPS, f);
1441   }
1442
1443   /**
1444    * Creates an SVG image of the alignment and writes it to the given file. If
1445    * the file is null, the user is prompted to choose a file.
1446    *
1447    * @param f
1448    */
1449   @Override
1450   public void createSVG(File f)
1451   {
1452     alignPanel.makeAlignmentImage(TYPE.SVG, f);
1453   }
1454
1455   @Override
1456   public void pageSetup_actionPerformed(ActionEvent e)
1457   {
1458     PrinterJob printJob = PrinterJob.getPrinterJob();
1459     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1460   }
1461
1462   /**
1463    * DOCUMENT ME!
1464    *
1465    * @param e
1466    *          DOCUMENT ME!
1467    */
1468   @Override
1469   public void printMenuItem_actionPerformed(ActionEvent e)
1470   {
1471     // Putting in a thread avoids Swing painting problems
1472     PrintThread thread = new PrintThread(alignPanel);
1473     thread.start();
1474   }
1475
1476   @Override
1477   public void exportFeatures_actionPerformed(ActionEvent e)
1478   {
1479     new AnnotationExporter(alignPanel).exportFeatures();
1480   }
1481
1482   @Override
1483   public void exportAnnotations_actionPerformed(ActionEvent e)
1484   {
1485     new AnnotationExporter(alignPanel).exportAnnotations();
1486   }
1487
1488   @Override
1489   public void associatedData_actionPerformed(ActionEvent e)
1490   {
1491     final JalviewFileChooser chooser = new JalviewFileChooser(
1492             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1493     chooser.setFileView(new JalviewFileView());
1494     chooser.setDialogTitle(
1495             MessageManager.getString("label.load_jalview_annotations"));
1496     chooser.setToolTipText(
1497             MessageManager.getString("label.load_jalview_annotations"));
1498     chooser.setResponseHandler(0, new Runnable()
1499     {
1500       @Override
1501       public void run()
1502       {
1503         String choice = chooser.getSelectedFile().getPath();
1504         jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1505         loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1506       }
1507     });
1508
1509     chooser.showOpenDialog(this);
1510   }
1511
1512   /**
1513    * Close the current view or all views in the alignment frame. If the frame
1514    * only contains one view then the alignment will be removed from memory.
1515    *
1516    * @param closeAllTabs
1517    */
1518   @Override
1519   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1520   {
1521     if (alignPanels != null && alignPanels.size() < 2)
1522     {
1523       closeAllTabs = true;
1524     }
1525
1526     try
1527     {
1528       if (alignPanels != null)
1529       {
1530         if (closeAllTabs)
1531         {
1532           if (this.isClosed())
1533           {
1534             // really close all the windows - otherwise wait till
1535             // setClosed(true) is called
1536             for (int i = 0; i < alignPanels.size(); i++)
1537             {
1538               AlignmentPanel ap = alignPanels.get(i);
1539               ap.closePanel();
1540             }
1541           }
1542         }
1543         else
1544         {
1545           closeView(alignPanel);
1546         }
1547       }
1548
1549       if (closeAllTabs)
1550       {
1551         /*
1552          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1553          * be called recursively, with the frame now in 'closed' state
1554          */
1555         this.setClosed(true);
1556       }
1557     } catch (Exception ex)
1558     {
1559       ex.printStackTrace();
1560     }
1561   }
1562
1563   /**
1564    * Close the specified panel and close up tabs appropriately.
1565    *
1566    * @param panelToClose
1567    */
1568   public void closeView(AlignmentPanel panelToClose)
1569   {
1570     int index = tabbedPane.getSelectedIndex();
1571     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1572     alignPanels.remove(panelToClose);
1573     panelToClose.closePanel();
1574     panelToClose = null;
1575
1576     tabbedPane.removeTabAt(closedindex);
1577     tabbedPane.validate();
1578
1579     if (index > closedindex || index == tabbedPane.getTabCount())
1580     {
1581       // modify currently selected tab index if necessary.
1582       index--;
1583     }
1584
1585     this.tabSelectionChanged(index);
1586   }
1587
1588   /**
1589    * DOCUMENT ME!
1590    */
1591   void updateEditMenuBar()
1592   {
1593
1594     if (viewport.getHistoryList().size() > 0)
1595     {
1596       undoMenuItem.setEnabled(true);
1597       CommandI command = viewport.getHistoryList().peek();
1598       undoMenuItem.setText(MessageManager
1599               .formatMessage("label.undo_command", new Object[]
1600               { command.getDescription() }));
1601     }
1602     else
1603     {
1604       undoMenuItem.setEnabled(false);
1605       undoMenuItem.setText(MessageManager.getString("action.undo"));
1606     }
1607
1608     if (viewport.getRedoList().size() > 0)
1609     {
1610       redoMenuItem.setEnabled(true);
1611
1612       CommandI command = viewport.getRedoList().peek();
1613       redoMenuItem.setText(MessageManager
1614               .formatMessage("label.redo_command", new Object[]
1615               { command.getDescription() }));
1616     }
1617     else
1618     {
1619       redoMenuItem.setEnabled(false);
1620       redoMenuItem.setText(MessageManager.getString("action.redo"));
1621     }
1622   }
1623
1624   @Override
1625   public void addHistoryItem(CommandI command)
1626   {
1627     if (command.getSize() > 0)
1628     {
1629       viewport.addToHistoryList(command);
1630       viewport.clearRedoList();
1631       updateEditMenuBar();
1632       viewport.updateHiddenColumns();
1633       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1634       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1635       // viewport.getColumnSelection()
1636       // .getHiddenColumns().size() > 0);
1637     }
1638   }
1639
1640   /**
1641    *
1642    * @return alignment objects for all views
1643    */
1644   AlignmentI[] getViewAlignments()
1645   {
1646     if (alignPanels != null)
1647     {
1648       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1649       int i = 0;
1650       for (AlignmentPanel ap : alignPanels)
1651       {
1652         als[i++] = ap.av.getAlignment();
1653       }
1654       return als;
1655     }
1656     if (viewport != null)
1657     {
1658       return new AlignmentI[] { viewport.getAlignment() };
1659     }
1660     return null;
1661   }
1662
1663   /**
1664    * DOCUMENT ME!
1665    *
1666    * @param e
1667    *          DOCUMENT ME!
1668    */
1669   @Override
1670   protected void undoMenuItem_actionPerformed(ActionEvent e)
1671   {
1672     if (viewport.getHistoryList().isEmpty())
1673     {
1674       return;
1675     }
1676     CommandI command = viewport.getHistoryList().pop();
1677     viewport.addToRedoList(command);
1678     command.undoCommand(getViewAlignments());
1679
1680     AlignmentViewport originalSource = getOriginatingSource(command);
1681     updateEditMenuBar();
1682
1683     if (originalSource != null)
1684     {
1685       if (originalSource != viewport)
1686       {
1687         Cache.log.warn(
1688                 "Implementation worry: mismatch of viewport origin for undo");
1689       }
1690       originalSource.updateHiddenColumns();
1691       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1692       // null
1693       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1694       // viewport.getColumnSelection()
1695       // .getHiddenColumns().size() > 0);
1696       originalSource.firePropertyChange("alignment", null,
1697               originalSource.getAlignment().getSequences());
1698     }
1699   }
1700
1701   /**
1702    * DOCUMENT ME!
1703    *
1704    * @param e
1705    *          DOCUMENT ME!
1706    */
1707   @Override
1708   protected void redoMenuItem_actionPerformed(ActionEvent e)
1709   {
1710     if (viewport.getRedoList().size() < 1)
1711     {
1712       return;
1713     }
1714
1715     CommandI command = viewport.getRedoList().pop();
1716     viewport.addToHistoryList(command);
1717     command.doCommand(getViewAlignments());
1718
1719     AlignmentViewport originalSource = getOriginatingSource(command);
1720     updateEditMenuBar();
1721
1722     if (originalSource != null)
1723     {
1724
1725       if (originalSource != viewport)
1726       {
1727         Cache.log.warn(
1728                 "Implementation worry: mismatch of viewport origin for redo");
1729       }
1730       originalSource.updateHiddenColumns();
1731       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1732       // null
1733       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1734       // viewport.getColumnSelection()
1735       // .getHiddenColumns().size() > 0);
1736       originalSource.firePropertyChange("alignment", null,
1737               originalSource.getAlignment().getSequences());
1738     }
1739   }
1740
1741   AlignmentViewport getOriginatingSource(CommandI command)
1742   {
1743     AlignmentViewport originalSource = null;
1744     // For sequence removal and addition, we need to fire
1745     // the property change event FROM the viewport where the
1746     // original alignment was altered
1747     AlignmentI al = null;
1748     if (command instanceof EditCommand)
1749     {
1750       EditCommand editCommand = (EditCommand) command;
1751       al = editCommand.getAlignment();
1752       List<Component> comps = PaintRefresher.components
1753               .get(viewport.getSequenceSetId());
1754
1755       for (Component comp : comps)
1756       {
1757         if (comp instanceof AlignmentPanel)
1758         {
1759           if (al == ((AlignmentPanel) comp).av.getAlignment())
1760           {
1761             originalSource = ((AlignmentPanel) comp).av;
1762             break;
1763           }
1764         }
1765       }
1766     }
1767
1768     if (originalSource == null)
1769     {
1770       // The original view is closed, we must validate
1771       // the current view against the closed view first
1772       if (al != null)
1773       {
1774         PaintRefresher.validateSequences(al, viewport.getAlignment());
1775       }
1776
1777       originalSource = viewport;
1778     }
1779
1780     return originalSource;
1781   }
1782
1783   /**
1784    * DOCUMENT ME!
1785    *
1786    * @param up
1787    *          DOCUMENT ME!
1788    */
1789   public void moveSelectedSequences(boolean up)
1790   {
1791     SequenceGroup sg = viewport.getSelectionGroup();
1792
1793     if (sg == null)
1794     {
1795       return;
1796     }
1797     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1798             viewport.getHiddenRepSequences(), up);
1799     alignPanel.paintAlignment(true, false);
1800   }
1801
1802   synchronized void slideSequences(boolean right, int size)
1803   {
1804     List<SequenceI> sg = new ArrayList<>();
1805     if (viewport.cursorMode)
1806     {
1807       sg.add(viewport.getAlignment()
1808               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1809     }
1810     else if (viewport.getSelectionGroup() != null
1811             && viewport.getSelectionGroup().getSize() != viewport
1812                     .getAlignment().getHeight())
1813     {
1814       sg = viewport.getSelectionGroup()
1815               .getSequences(viewport.getHiddenRepSequences());
1816     }
1817
1818     if (sg.size() < 1)
1819     {
1820       return;
1821     }
1822
1823     List<SequenceI> invertGroup = new ArrayList<>();
1824
1825     for (SequenceI seq : viewport.getAlignment().getSequences())
1826     {
1827       if (!sg.contains(seq))
1828       {
1829         invertGroup.add(seq);
1830       }
1831     }
1832
1833     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1834
1835     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1836     for (int i = 0; i < invertGroup.size(); i++)
1837     {
1838       seqs2[i] = invertGroup.get(i);
1839     }
1840
1841     SlideSequencesCommand ssc;
1842     if (right)
1843     {
1844       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1845               viewport.getGapCharacter());
1846     }
1847     else
1848     {
1849       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1850               viewport.getGapCharacter());
1851     }
1852
1853     int groupAdjustment = 0;
1854     if (ssc.getGapsInsertedBegin() && right)
1855     {
1856       if (viewport.cursorMode)
1857       {
1858         alignPanel.getSeqPanel().moveCursor(size, 0);
1859       }
1860       else
1861       {
1862         groupAdjustment = size;
1863       }
1864     }
1865     else if (!ssc.getGapsInsertedBegin() && !right)
1866     {
1867       if (viewport.cursorMode)
1868       {
1869         alignPanel.getSeqPanel().moveCursor(-size, 0);
1870       }
1871       else
1872       {
1873         groupAdjustment = -size;
1874       }
1875     }
1876
1877     if (groupAdjustment != 0)
1878     {
1879       viewport.getSelectionGroup().setStartRes(
1880               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1881       viewport.getSelectionGroup().setEndRes(
1882               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1883     }
1884
1885     /*
1886      * just extend the last slide command if compatible; but not if in
1887      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1888      */
1889     boolean appendHistoryItem = false;
1890     Deque<CommandI> historyList = viewport.getHistoryList();
1891     boolean inSplitFrame = getSplitViewContainer() != null;
1892     if (!inSplitFrame && historyList != null && historyList.size() > 0
1893             && historyList.peek() instanceof SlideSequencesCommand)
1894     {
1895       appendHistoryItem = ssc.appendSlideCommand(
1896               (SlideSequencesCommand) historyList.peek());
1897     }
1898
1899     if (!appendHistoryItem)
1900     {
1901       addHistoryItem(ssc);
1902     }
1903
1904     repaint();
1905   }
1906
1907   /**
1908    * DOCUMENT ME!
1909    *
1910    * @param e
1911    *          DOCUMENT ME!
1912    */
1913   @Override
1914   protected void copy_actionPerformed()
1915   {
1916     if (viewport.getSelectionGroup() == null)
1917     {
1918       return;
1919     }
1920     // TODO: preserve the ordering of displayed alignment annotation in any
1921     // internal paste (particularly sequence associated annotation)
1922     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1923     String[] omitHidden = null;
1924
1925     if (viewport.hasHiddenColumns())
1926     {
1927       omitHidden = viewport.getViewAsString(true);
1928     }
1929
1930     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1931             seqs, omitHidden, null);
1932
1933     StringSelection ss = new StringSelection(output);
1934
1935     try
1936     {
1937       jalview.gui.Desktop.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               Desktop.instance);
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     Desktop.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       if (Desktop.jalviewClipboard != null)
2037       {
2038         // The clipboard was filled from within Jalview, we must use the
2039         // sequences
2040         // And dataset from the copied alignment
2041         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2042         // be doubly sure that we create *new* sequence objects.
2043         sequences = new SequenceI[newseq.length];
2044         for (int i = 0; i < newseq.length; i++)
2045         {
2046           sequences[i] = new Sequence(newseq[i]);
2047         }
2048         alignment = new Alignment(sequences);
2049         externalPaste = false;
2050       }
2051       else
2052       {
2053         // parse the clipboard as an alignment.
2054         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2055                 format);
2056         sequences = alignment.getSequencesArray();
2057       }
2058
2059       int alwidth = 0;
2060       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2061       int fgroup = -1;
2062
2063       if (newAlignment)
2064       {
2065
2066         if (Desktop.jalviewClipboard != null)
2067         {
2068           // dataset is inherited
2069           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2070         }
2071         else
2072         {
2073           // new dataset is constructed
2074           alignment.setDataset(null);
2075         }
2076         alwidth = alignment.getWidth() + 1;
2077       }
2078       else
2079       {
2080         AlignmentI pastedal = alignment; // preserve pasted alignment object
2081         // Add pasted sequences and dataset into existing alignment.
2082         alignment = viewport.getAlignment();
2083         alwidth = alignment.getWidth() + 1;
2084         // decide if we need to import sequences from an existing dataset
2085         boolean importDs = Desktop.jalviewClipboard != null
2086                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2087         // importDs==true instructs us to copy over new dataset sequences from
2088         // an existing alignment
2089         Vector newDs = (importDs) ? new Vector() : null; // used to create
2090         // minimum dataset set
2091
2092         for (int i = 0; i < sequences.length; i++)
2093         {
2094           if (importDs)
2095           {
2096             newDs.addElement(null);
2097           }
2098           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2099           // paste
2100           if (importDs && ds != null)
2101           {
2102             if (!newDs.contains(ds))
2103             {
2104               newDs.setElementAt(ds, i);
2105               ds = new Sequence(ds);
2106               // update with new dataset sequence
2107               sequences[i].setDatasetSequence(ds);
2108             }
2109             else
2110             {
2111               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2112             }
2113           }
2114           else
2115           {
2116             // copy and derive new dataset sequence
2117             sequences[i] = sequences[i].deriveSequence();
2118             alignment.getDataset()
2119                     .addSequence(sequences[i].getDatasetSequence());
2120             // TODO: avoid creation of duplicate dataset sequences with a
2121             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2122           }
2123           alignment.addSequence(sequences[i]); // merges dataset
2124         }
2125         if (newDs != null)
2126         {
2127           newDs.clear(); // tidy up
2128         }
2129         if (alignment.getAlignmentAnnotation() != null)
2130         {
2131           for (AlignmentAnnotation alan : alignment
2132                   .getAlignmentAnnotation())
2133           {
2134             if (alan.graphGroup > fgroup)
2135             {
2136               fgroup = alan.graphGroup;
2137             }
2138           }
2139         }
2140         if (pastedal.getAlignmentAnnotation() != null)
2141         {
2142           // Add any annotation attached to alignment.
2143           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2144           for (int i = 0; i < alann.length; i++)
2145           {
2146             annotationAdded = true;
2147             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2148             {
2149               AlignmentAnnotation newann = new AlignmentAnnotation(
2150                       alann[i]);
2151               if (newann.graphGroup > -1)
2152               {
2153                 if (newGraphGroups.size() <= newann.graphGroup
2154                         || newGraphGroups.get(newann.graphGroup) == null)
2155                 {
2156                   for (int q = newGraphGroups
2157                           .size(); q <= newann.graphGroup; q++)
2158                   {
2159                     newGraphGroups.add(q, null);
2160                   }
2161                   newGraphGroups.set(newann.graphGroup,
2162                           new Integer(++fgroup));
2163                 }
2164                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2165                         .intValue();
2166               }
2167
2168               newann.padAnnotation(alwidth);
2169               alignment.addAnnotation(newann);
2170             }
2171           }
2172         }
2173       }
2174       if (!newAlignment)
2175       {
2176         // /////
2177         // ADD HISTORY ITEM
2178         //
2179         addHistoryItem(new EditCommand(
2180                 MessageManager.getString("label.add_sequences"),
2181                 Action.PASTE, sequences, 0, alignment.getWidth(),
2182                 alignment));
2183       }
2184       // Add any annotations attached to sequences
2185       for (int i = 0; i < sequences.length; i++)
2186       {
2187         if (sequences[i].getAnnotation() != null)
2188         {
2189           AlignmentAnnotation newann;
2190           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2191           {
2192             annotationAdded = true;
2193             newann = sequences[i].getAnnotation()[a];
2194             newann.adjustForAlignment();
2195             newann.padAnnotation(alwidth);
2196             if (newann.graphGroup > -1)
2197             {
2198               if (newann.graphGroup > -1)
2199               {
2200                 if (newGraphGroups.size() <= newann.graphGroup
2201                         || newGraphGroups.get(newann.graphGroup) == null)
2202                 {
2203                   for (int q = newGraphGroups
2204                           .size(); q <= newann.graphGroup; q++)
2205                   {
2206                     newGraphGroups.add(q, null);
2207                   }
2208                   newGraphGroups.set(newann.graphGroup,
2209                           new Integer(++fgroup));
2210                 }
2211                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2212                         .intValue();
2213               }
2214             }
2215             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2216             // was
2217             // duplicated
2218             // earlier
2219             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2220                     a);
2221           }
2222         }
2223       }
2224       if (!newAlignment)
2225       {
2226
2227         // propagate alignment changed.
2228         viewport.getRanges().setEndSeq(alignment.getHeight());
2229         if (annotationAdded)
2230         {
2231           // Duplicate sequence annotation in all views.
2232           AlignmentI[] alview = this.getViewAlignments();
2233           for (int i = 0; i < sequences.length; i++)
2234           {
2235             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2236             if (sann == null)
2237             {
2238               continue;
2239             }
2240             for (int avnum = 0; avnum < alview.length; avnum++)
2241             {
2242               if (alview[avnum] != alignment)
2243               {
2244                 // duplicate in a view other than the one with input focus
2245                 int avwidth = alview[avnum].getWidth() + 1;
2246                 // this relies on sann being preserved after we
2247                 // modify the sequence's annotation array for each duplication
2248                 for (int a = 0; a < sann.length; a++)
2249                 {
2250                   AlignmentAnnotation newann = new AlignmentAnnotation(
2251                           sann[a]);
2252                   sequences[i].addAlignmentAnnotation(newann);
2253                   newann.padAnnotation(avwidth);
2254                   alview[avnum].addAnnotation(newann); // annotation was
2255                   // duplicated earlier
2256                   // TODO JAL-1145 graphGroups are not updated for sequence
2257                   // annotation added to several views. This may cause
2258                   // strangeness
2259                   alview[avnum].setAnnotationIndex(newann, a);
2260                 }
2261               }
2262             }
2263           }
2264           buildSortByAnnotationScoresMenu();
2265         }
2266         viewport.firePropertyChange("alignment", null,
2267                 alignment.getSequences());
2268         if (alignPanels != null)
2269         {
2270           for (AlignmentPanel ap : alignPanels)
2271           {
2272             ap.validateAnnotationDimensions(false);
2273           }
2274         }
2275         else
2276         {
2277           alignPanel.validateAnnotationDimensions(false);
2278         }
2279
2280       }
2281       else
2282       {
2283         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2284                 DEFAULT_HEIGHT);
2285         String newtitle = new String("Copied sequences");
2286
2287         if (Desktop.jalviewClipboard != null
2288                 && Desktop.jalviewClipboard[2] != null)
2289         {
2290           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2291           af.viewport.setHiddenColumns(hc);
2292         }
2293
2294         // >>>This is a fix for the moment, until a better solution is
2295         // found!!<<<
2296         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2297                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2298                         .getFeatureRenderer());
2299
2300         // TODO: maintain provenance of an alignment, rather than just make the
2301         // title a concatenation of operations.
2302         if (!externalPaste)
2303         {
2304           if (title.startsWith("Copied sequences"))
2305           {
2306             newtitle = title;
2307           }
2308           else
2309           {
2310             newtitle = newtitle.concat("- from " + title);
2311           }
2312         }
2313         else
2314         {
2315           newtitle = new String("Pasted sequences");
2316         }
2317
2318         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2319                 DEFAULT_HEIGHT);
2320
2321       }
2322
2323     } catch (Exception ex)
2324     {
2325       ex.printStackTrace();
2326       System.out.println("Exception whilst pasting: " + ex);
2327       // could be anything being pasted in here
2328     }
2329
2330   }
2331
2332   @Override
2333   protected void expand_newalign(ActionEvent e)
2334   {
2335     try
2336     {
2337       AlignmentI alignment = AlignmentUtils
2338               .expandContext(getViewport().getAlignment(), -1);
2339       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2340               DEFAULT_HEIGHT);
2341       String newtitle = new String("Flanking alignment");
2342
2343       if (Desktop.jalviewClipboard != null
2344               && Desktop.jalviewClipboard[2] != null)
2345       {
2346         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2347         af.viewport.setHiddenColumns(hc);
2348       }
2349
2350       // >>>This is a fix for the moment, until a better solution is
2351       // found!!<<<
2352       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2353               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2354                       .getFeatureRenderer());
2355
2356       // TODO: maintain provenance of an alignment, rather than just make the
2357       // title a concatenation of operations.
2358       {
2359         if (title.startsWith("Copied sequences"))
2360         {
2361           newtitle = title;
2362         }
2363         else
2364         {
2365           newtitle = newtitle.concat("- from " + title);
2366         }
2367       }
2368
2369       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2370
2371     } catch (Exception ex)
2372     {
2373       ex.printStackTrace();
2374       System.out.println("Exception whilst pasting: " + ex);
2375       // could be anything being pasted in here
2376     } catch (OutOfMemoryError oom)
2377     {
2378       new OOMWarning("Viewing flanking region of alignment", oom);
2379     }
2380   }
2381
2382   /**
2383    * Action Cut (delete and copy) the selected region
2384    */
2385   @Override
2386   protected void cut_actionPerformed()
2387   {
2388     copy_actionPerformed();
2389     delete_actionPerformed();
2390   }
2391
2392   /**
2393    * Performs menu option to Delete the currently selected region
2394    */
2395   @Override
2396   protected void delete_actionPerformed()
2397   {
2398
2399     SequenceGroup sg = viewport.getSelectionGroup();
2400     if (sg == null)
2401     {
2402       return;
2403     }
2404
2405     Runnable okAction = new Runnable()
2406     {
2407                 @Override
2408                 public void run()
2409                 {
2410                     SequenceI[] cut = sg.getSequences()
2411                             .toArray(new SequenceI[sg.getSize()]);
2412
2413                     addHistoryItem(new EditCommand(
2414                             MessageManager.getString("label.cut_sequences"), Action.CUT,
2415                             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2416                             viewport.getAlignment()));
2417
2418                     viewport.setSelectionGroup(null);
2419                     viewport.sendSelection();
2420                     viewport.getAlignment().deleteGroup(sg);
2421
2422                     viewport.firePropertyChange("alignment", null,
2423                             viewport.getAlignment().getSequences());
2424                     if (viewport.getAlignment().getHeight() < 1)
2425                     {
2426                       try
2427                       {
2428                         AlignFrame.this.setClosed(true);
2429                       } catch (Exception ex)
2430                       {
2431                       }
2432                     }
2433                 }};
2434
2435     /*
2436      * If the cut affects all sequences, prompt for confirmation
2437      */
2438     boolean wholeHeight = sg.getSize() == viewport.getAlignment().getHeight();
2439     boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2440             + 1) == viewport.getAlignment().getWidth()) ? true : false;
2441         if (wholeHeight && wholeWidth)
2442         {
2443             JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
2444                 dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2445             Object[] options = new Object[] { MessageManager.getString("action.ok"),
2446                     MessageManager.getString("action.cancel") };
2447                 dialog.showDialog(MessageManager.getString("warn.delete_all"),
2448                     MessageManager.getString("label.delete_all"),
2449                     JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2450                     options, options[0]);
2451         } else
2452         {
2453                 okAction.run();
2454         }
2455   }
2456
2457   /**
2458    * DOCUMENT ME!
2459    *
2460    * @param e
2461    *          DOCUMENT ME!
2462    */
2463   @Override
2464   protected void deleteGroups_actionPerformed(ActionEvent e)
2465   {
2466     if (avc.deleteGroups())
2467     {
2468       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2469       alignPanel.updateAnnotation();
2470       alignPanel.paintAlignment(true, true);
2471     }
2472   }
2473
2474   /**
2475    * DOCUMENT ME!
2476    *
2477    * @param e
2478    *          DOCUMENT ME!
2479    */
2480   @Override
2481   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2482   {
2483     SequenceGroup sg = new SequenceGroup(
2484             viewport.getAlignment().getSequences());
2485
2486     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2487     viewport.setSelectionGroup(sg);
2488     viewport.isSelectionGroupChanged(true);
2489     viewport.sendSelection();
2490     // JAL-2034 - should delegate to
2491     // alignPanel to decide if overview needs
2492     // updating.
2493     alignPanel.paintAlignment(false, false);
2494     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2495   }
2496
2497   /**
2498    * DOCUMENT ME!
2499    *
2500    * @param e
2501    *          DOCUMENT ME!
2502    */
2503   @Override
2504   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2505   {
2506     if (viewport.cursorMode)
2507     {
2508       alignPanel.getSeqPanel().keyboardNo1 = null;
2509       alignPanel.getSeqPanel().keyboardNo2 = null;
2510     }
2511     viewport.setSelectionGroup(null);
2512     viewport.getColumnSelection().clear();
2513     viewport.setSelectionGroup(null);
2514     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2515     // JAL-2034 - should delegate to
2516     // alignPanel to decide if overview needs
2517     // updating.
2518     alignPanel.paintAlignment(false, false);
2519     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2520     viewport.sendSelection();
2521   }
2522
2523   /**
2524    * DOCUMENT ME!
2525    *
2526    * @param e
2527    *          DOCUMENT ME!
2528    */
2529   @Override
2530   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2531   {
2532     SequenceGroup sg = viewport.getSelectionGroup();
2533
2534     if (sg == null)
2535     {
2536       selectAllSequenceMenuItem_actionPerformed(null);
2537
2538       return;
2539     }
2540
2541     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2542     {
2543       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2544     }
2545     // JAL-2034 - should delegate to
2546     // alignPanel to decide if overview needs
2547     // updating.
2548
2549     alignPanel.paintAlignment(true, false);
2550     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2551     viewport.sendSelection();
2552   }
2553
2554   @Override
2555   public void invertColSel_actionPerformed(ActionEvent e)
2556   {
2557     viewport.invertColumnSelection();
2558     alignPanel.paintAlignment(true, false);
2559     viewport.sendSelection();
2560   }
2561
2562   /**
2563    * DOCUMENT ME!
2564    *
2565    * @param e
2566    *          DOCUMENT ME!
2567    */
2568   @Override
2569   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2570   {
2571     trimAlignment(true);
2572   }
2573
2574   /**
2575    * DOCUMENT ME!
2576    *
2577    * @param e
2578    *          DOCUMENT ME!
2579    */
2580   @Override
2581   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2582   {
2583     trimAlignment(false);
2584   }
2585
2586   void trimAlignment(boolean trimLeft)
2587   {
2588     ColumnSelection colSel = viewport.getColumnSelection();
2589     int column;
2590
2591     if (!colSel.isEmpty())
2592     {
2593       if (trimLeft)
2594       {
2595         column = colSel.getMin();
2596       }
2597       else
2598       {
2599         column = colSel.getMax();
2600       }
2601
2602       SequenceI[] seqs;
2603       if (viewport.getSelectionGroup() != null)
2604       {
2605         seqs = viewport.getSelectionGroup()
2606                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2607       }
2608       else
2609       {
2610         seqs = viewport.getAlignment().getSequencesArray();
2611       }
2612
2613       TrimRegionCommand trimRegion;
2614       if (trimLeft)
2615       {
2616         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2617                 column, viewport.getAlignment());
2618         viewport.getRanges().setStartRes(0);
2619       }
2620       else
2621       {
2622         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2623                 column, viewport.getAlignment());
2624       }
2625
2626       setStatus(MessageManager
2627               .formatMessage("label.removed_columns", new String[]
2628               { Integer.valueOf(trimRegion.getSize()).toString() }));
2629
2630       addHistoryItem(trimRegion);
2631
2632       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2633       {
2634         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2635                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2636         {
2637           viewport.getAlignment().deleteGroup(sg);
2638         }
2639       }
2640
2641       viewport.firePropertyChange("alignment", null,
2642               viewport.getAlignment().getSequences());
2643     }
2644   }
2645
2646   /**
2647    * DOCUMENT ME!
2648    *
2649    * @param e
2650    *          DOCUMENT ME!
2651    */
2652   @Override
2653   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2654   {
2655     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2656
2657     SequenceI[] seqs;
2658     if (viewport.getSelectionGroup() != null)
2659     {
2660       seqs = viewport.getSelectionGroup()
2661               .getSequencesAsArray(viewport.getHiddenRepSequences());
2662       start = viewport.getSelectionGroup().getStartRes();
2663       end = viewport.getSelectionGroup().getEndRes();
2664     }
2665     else
2666     {
2667       seqs = viewport.getAlignment().getSequencesArray();
2668     }
2669
2670     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2671             "Remove Gapped Columns", seqs, start, end,
2672             viewport.getAlignment());
2673
2674     addHistoryItem(removeGapCols);
2675
2676     setStatus(MessageManager
2677             .formatMessage("label.removed_empty_columns", new Object[]
2678             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2679
2680     // This is to maintain viewport position on first residue
2681     // of first sequence
2682     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2683     ViewportRanges ranges = viewport.getRanges();
2684     int startRes = seq.findPosition(ranges.getStartRes());
2685     // ShiftList shifts;
2686     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2687     // edit.alColumnChanges=shifts.getInverse();
2688     // if (viewport.hasHiddenColumns)
2689     // viewport.getColumnSelection().compensateForEdits(shifts);
2690     ranges.setStartRes(seq.findIndex(startRes) - 1);
2691     viewport.firePropertyChange("alignment", null,
2692             viewport.getAlignment().getSequences());
2693
2694   }
2695
2696   /**
2697    * DOCUMENT ME!
2698    *
2699    * @param e
2700    *          DOCUMENT ME!
2701    */
2702   @Override
2703   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2704   {
2705     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2706
2707     SequenceI[] seqs;
2708     if (viewport.getSelectionGroup() != null)
2709     {
2710       seqs = viewport.getSelectionGroup()
2711               .getSequencesAsArray(viewport.getHiddenRepSequences());
2712       start = viewport.getSelectionGroup().getStartRes();
2713       end = viewport.getSelectionGroup().getEndRes();
2714     }
2715     else
2716     {
2717       seqs = viewport.getAlignment().getSequencesArray();
2718     }
2719
2720     // This is to maintain viewport position on first residue
2721     // of first sequence
2722     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2723     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2724
2725     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2726             viewport.getAlignment()));
2727
2728     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2729
2730     viewport.firePropertyChange("alignment", null,
2731             viewport.getAlignment().getSequences());
2732
2733   }
2734
2735   /**
2736    * DOCUMENT ME!
2737    *
2738    * @param e
2739    *          DOCUMENT ME!
2740    */
2741   @Override
2742   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2743   {
2744     viewport.setPadGaps(padGapsMenuitem.isSelected());
2745     viewport.firePropertyChange("alignment", null,
2746             viewport.getAlignment().getSequences());
2747   }
2748
2749   /**
2750    * DOCUMENT ME!
2751    *
2752    * @param e
2753    *          DOCUMENT ME!
2754    */
2755   @Override
2756   public void findMenuItem_actionPerformed(ActionEvent e)
2757   {
2758     new Finder();
2759   }
2760
2761   /**
2762    * Create a new view of the current alignment.
2763    */
2764   @Override
2765   public void newView_actionPerformed(ActionEvent e)
2766   {
2767     newView(null, true);
2768   }
2769
2770   /**
2771    * Creates and shows a new view of the current alignment.
2772    *
2773    * @param viewTitle
2774    *          title of newly created view; if null, one will be generated
2775    * @param copyAnnotation
2776    *          if true then duplicate all annnotation, groups and settings
2777    * @return new alignment panel, already displayed.
2778    */
2779   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2780   {
2781     /*
2782      * Create a new AlignmentPanel (with its own, new Viewport)
2783      */
2784     AlignmentPanel newap = new jalview.project.Jalview2XML()
2785             .copyAlignPanel(alignPanel);
2786     if (!copyAnnotation)
2787     {
2788       /*
2789        * remove all groups and annotation except for the automatic stuff
2790        */
2791       newap.av.getAlignment().deleteAllGroups();
2792       newap.av.getAlignment().deleteAllAnnotations(false);
2793     }
2794
2795     newap.av.setGatherViewsHere(false);
2796
2797     if (viewport.getViewName() == null)
2798     {
2799       viewport.setViewName(MessageManager
2800               .getString("label.view_name_original"));
2801     }
2802
2803     /*
2804      * Views share the same edits undo and redo stacks
2805      */
2806     newap.av.setHistoryList(viewport.getHistoryList());
2807     newap.av.setRedoList(viewport.getRedoList());
2808
2809     /*
2810      * copy any visualisation settings that are not saved in the project
2811      */
2812     newap.av.setColourAppliesToAllGroups(
2813             viewport.getColourAppliesToAllGroups());
2814
2815     /*
2816      * Views share the same mappings; need to deregister any new mappings
2817      * created by copyAlignPanel, and register the new reference to the shared
2818      * mappings
2819      */
2820     newap.av.replaceMappings(viewport.getAlignment());
2821
2822     /*
2823      * start up cDNA consensus (if applicable) now mappings are in place
2824      */
2825     if (newap.av.initComplementConsensus())
2826     {
2827       newap.refresh(true); // adjust layout of annotations
2828     }
2829
2830     newap.av.setViewName(getNewViewName(viewTitle));
2831
2832     addAlignmentPanel(newap, true);
2833     newap.alignmentChanged();
2834
2835     if (alignPanels.size() == 2)
2836     {
2837       viewport.setGatherViewsHere(true);
2838     }
2839     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2840     return newap;
2841   }
2842
2843   /**
2844    * Make a new name for the view, ensuring it is unique within the current
2845    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2846    * these now use viewId. Unique view names are still desirable for usability.)
2847    *
2848    * @param viewTitle
2849    * @return
2850    */
2851   protected String getNewViewName(String viewTitle)
2852   {
2853     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2854     boolean addFirstIndex = false;
2855     if (viewTitle == null || viewTitle.trim().length() == 0)
2856     {
2857       viewTitle = MessageManager.getString("action.view");
2858       addFirstIndex = true;
2859     }
2860     else
2861     {
2862       index = 1;// we count from 1 if given a specific name
2863     }
2864     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2865
2866     List<Component> comps = PaintRefresher.components
2867             .get(viewport.getSequenceSetId());
2868
2869     List<String> existingNames = getExistingViewNames(comps);
2870
2871     while (existingNames.contains(newViewName))
2872     {
2873       newViewName = viewTitle + " " + (++index);
2874     }
2875     return newViewName;
2876   }
2877
2878   /**
2879    * Returns a list of distinct view names found in the given list of
2880    * components. View names are held on the viewport of an AlignmentPanel.
2881    *
2882    * @param comps
2883    * @return
2884    */
2885   protected List<String> getExistingViewNames(List<Component> comps)
2886   {
2887     List<String> existingNames = new ArrayList<>();
2888     for (Component comp : comps)
2889     {
2890       if (comp instanceof AlignmentPanel)
2891       {
2892         AlignmentPanel ap = (AlignmentPanel) comp;
2893         if (!existingNames.contains(ap.av.getViewName()))
2894         {
2895           existingNames.add(ap.av.getViewName());
2896         }
2897       }
2898     }
2899     return existingNames;
2900   }
2901
2902   /**
2903    * Explode tabbed views into separate windows.
2904    */
2905   @Override
2906   public void expandViews_actionPerformed(ActionEvent e)
2907   {
2908     Desktop.explodeViews(this);
2909   }
2910
2911   /**
2912    * Gather views in separate windows back into a tabbed presentation.
2913    */
2914   @Override
2915   public void gatherViews_actionPerformed(ActionEvent e)
2916   {
2917     Desktop.instance.gatherViews(this);
2918   }
2919
2920   /**
2921    * DOCUMENT ME!
2922    *
2923    * @param e
2924    *          DOCUMENT ME!
2925    */
2926   @Override
2927   public void font_actionPerformed(ActionEvent e)
2928   {
2929     new FontChooser(alignPanel);
2930   }
2931
2932   /**
2933    * DOCUMENT ME!
2934    *
2935    * @param e
2936    *          DOCUMENT ME!
2937    */
2938   @Override
2939   protected void seqLimit_actionPerformed(ActionEvent e)
2940   {
2941     viewport.setShowJVSuffix(seqLimits.isSelected());
2942
2943     alignPanel.getIdPanel().getIdCanvas()
2944             .setPreferredSize(alignPanel.calculateIdWidth());
2945     alignPanel.paintAlignment(true, false);
2946   }
2947
2948   @Override
2949   public void idRightAlign_actionPerformed(ActionEvent e)
2950   {
2951     viewport.setRightAlignIds(idRightAlign.isSelected());
2952     alignPanel.paintAlignment(false, false);
2953   }
2954
2955   @Override
2956   public void centreColumnLabels_actionPerformed(ActionEvent e)
2957   {
2958     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2959     alignPanel.paintAlignment(false, false);
2960   }
2961
2962   /*
2963    * (non-Javadoc)
2964    *
2965    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2966    */
2967   @Override
2968   protected void followHighlight_actionPerformed()
2969   {
2970     /*
2971      * Set the 'follow' flag on the Viewport (and scroll to position if now
2972      * true).
2973      */
2974     final boolean state = this.followHighlightMenuItem.getState();
2975     viewport.setFollowHighlight(state);
2976     if (state)
2977     {
2978       alignPanel.scrollToPosition(viewport.getSearchResults());
2979     }
2980   }
2981
2982   /**
2983    * DOCUMENT ME!
2984    *
2985    * @param e
2986    *          DOCUMENT ME!
2987    */
2988   @Override
2989   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2990   {
2991     viewport.setColourText(colourTextMenuItem.isSelected());
2992     alignPanel.paintAlignment(false, false);
2993   }
2994
2995   /**
2996    * DOCUMENT ME!
2997    *
2998    * @param e
2999    *          DOCUMENT ME!
3000    */
3001   @Override
3002   public void wrapMenuItem_actionPerformed(ActionEvent e)
3003   {
3004     scaleAbove.setVisible(wrapMenuItem.isSelected());
3005     scaleLeft.setVisible(wrapMenuItem.isSelected());
3006     scaleRight.setVisible(wrapMenuItem.isSelected());
3007     viewport.setWrapAlignment(wrapMenuItem.isSelected());
3008     alignPanel.updateLayout();
3009   }
3010
3011   @Override
3012   public void showAllSeqs_actionPerformed(ActionEvent e)
3013   {
3014     viewport.showAllHiddenSeqs();
3015   }
3016
3017   @Override
3018   public void showAllColumns_actionPerformed(ActionEvent e)
3019   {
3020     viewport.showAllHiddenColumns();
3021     alignPanel.paintAlignment(true, true);
3022     viewport.sendSelection();
3023   }
3024
3025   @Override
3026   public void hideSelSequences_actionPerformed(ActionEvent e)
3027   {
3028     viewport.hideAllSelectedSeqs();
3029   }
3030
3031   /**
3032    * called by key handler and the hide all/show all menu items
3033    *
3034    * @param toggleSeqs
3035    * @param toggleCols
3036    */
3037   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3038   {
3039
3040     boolean hide = false;
3041     SequenceGroup sg = viewport.getSelectionGroup();
3042     if (!toggleSeqs && !toggleCols)
3043     {
3044       // Hide everything by the current selection - this is a hack - we do the
3045       // invert and then hide
3046       // first check that there will be visible columns after the invert.
3047       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3048               && sg.getStartRes() <= sg.getEndRes()))
3049       {
3050         // now invert the sequence set, if required - empty selection implies
3051         // that no hiding is required.
3052         if (sg != null)
3053         {
3054           invertSequenceMenuItem_actionPerformed(null);
3055           sg = viewport.getSelectionGroup();
3056           toggleSeqs = true;
3057
3058         }
3059         viewport.expandColSelection(sg, true);
3060         // finally invert the column selection and get the new sequence
3061         // selection.
3062         invertColSel_actionPerformed(null);
3063         toggleCols = true;
3064       }
3065     }
3066
3067     if (toggleSeqs)
3068     {
3069       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3070       {
3071         hideSelSequences_actionPerformed(null);
3072         hide = true;
3073       }
3074       else if (!(toggleCols && viewport.hasSelectedColumns()))
3075       {
3076         showAllSeqs_actionPerformed(null);
3077       }
3078     }
3079
3080     if (toggleCols)
3081     {
3082       if (viewport.hasSelectedColumns())
3083       {
3084         hideSelColumns_actionPerformed(null);
3085         if (!toggleSeqs)
3086         {
3087           viewport.setSelectionGroup(sg);
3088         }
3089       }
3090       else if (!hide)
3091       {
3092         showAllColumns_actionPerformed(null);
3093       }
3094     }
3095   }
3096
3097   /*
3098    * (non-Javadoc)
3099    *
3100    * @see
3101    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3102    * event.ActionEvent)
3103    */
3104   @Override
3105   public void hideAllButSelection_actionPerformed(ActionEvent e)
3106   {
3107     toggleHiddenRegions(false, false);
3108     viewport.sendSelection();
3109   }
3110
3111   /*
3112    * (non-Javadoc)
3113    *
3114    * @see
3115    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3116    * .ActionEvent)
3117    */
3118   @Override
3119   public void hideAllSelection_actionPerformed(ActionEvent e)
3120   {
3121     SequenceGroup sg = viewport.getSelectionGroup();
3122     viewport.expandColSelection(sg, false);
3123     viewport.hideAllSelectedSeqs();
3124     viewport.hideSelectedColumns();
3125     alignPanel.updateLayout();
3126     alignPanel.paintAlignment(true, true);
3127     viewport.sendSelection();
3128   }
3129
3130   /*
3131    * (non-Javadoc)
3132    *
3133    * @see
3134    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3135    * ActionEvent)
3136    */
3137   @Override
3138   public void showAllhidden_actionPerformed(ActionEvent e)
3139   {
3140     viewport.showAllHiddenColumns();
3141     viewport.showAllHiddenSeqs();
3142     alignPanel.paintAlignment(true, true);
3143     viewport.sendSelection();
3144   }
3145
3146   @Override
3147   public void hideSelColumns_actionPerformed(ActionEvent e)
3148   {
3149     viewport.hideSelectedColumns();
3150     alignPanel.updateLayout();
3151     alignPanel.paintAlignment(true, true);
3152     viewport.sendSelection();
3153   }
3154
3155   @Override
3156   public void hiddenMarkers_actionPerformed(ActionEvent e)
3157   {
3158     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3159     repaint();
3160   }
3161
3162   /**
3163    * DOCUMENT ME!
3164    *
3165    * @param e
3166    *          DOCUMENT ME!
3167    */
3168   @Override
3169   protected void scaleAbove_actionPerformed(ActionEvent e)
3170   {
3171     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3172     alignPanel.updateLayout();
3173     alignPanel.paintAlignment(true, false);
3174   }
3175
3176   /**
3177    * DOCUMENT ME!
3178    *
3179    * @param e
3180    *          DOCUMENT ME!
3181    */
3182   @Override
3183   protected void scaleLeft_actionPerformed(ActionEvent e)
3184   {
3185     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3186     alignPanel.updateLayout();
3187     alignPanel.paintAlignment(true, false);
3188   }
3189
3190   /**
3191    * DOCUMENT ME!
3192    *
3193    * @param e
3194    *          DOCUMENT ME!
3195    */
3196   @Override
3197   protected void scaleRight_actionPerformed(ActionEvent e)
3198   {
3199     viewport.setScaleRightWrapped(scaleRight.isSelected());
3200     alignPanel.updateLayout();
3201     alignPanel.paintAlignment(true, false);
3202   }
3203
3204   /**
3205    * DOCUMENT ME!
3206    *
3207    * @param e
3208    *          DOCUMENT ME!
3209    */
3210   @Override
3211   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3212   {
3213     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3214     alignPanel.paintAlignment(false, false);
3215   }
3216
3217   /**
3218    * DOCUMENT ME!
3219    *
3220    * @param e
3221    *          DOCUMENT ME!
3222    */
3223   @Override
3224   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3225   {
3226     viewport.setShowText(viewTextMenuItem.isSelected());
3227     alignPanel.paintAlignment(false, false);
3228   }
3229
3230   /**
3231    * DOCUMENT ME!
3232    *
3233    * @param e
3234    *          DOCUMENT ME!
3235    */
3236   @Override
3237   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3238   {
3239     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3240     alignPanel.paintAlignment(false, false);
3241   }
3242
3243   public FeatureSettings featureSettings;
3244
3245   @Override
3246   public FeatureSettingsControllerI getFeatureSettingsUI()
3247   {
3248     return featureSettings;
3249   }
3250
3251   @Override
3252   public void featureSettings_actionPerformed(ActionEvent e)
3253   {
3254     if (featureSettings != null)
3255     {
3256       featureSettings.close();
3257       featureSettings = null;
3258     }
3259     if (!showSeqFeatures.isSelected())
3260     {
3261       // make sure features are actually displayed
3262       showSeqFeatures.setSelected(true);
3263       showSeqFeatures_actionPerformed(null);
3264     }
3265     featureSettings = new FeatureSettings(this);
3266   }
3267
3268   /**
3269    * Set or clear 'Show Sequence Features'
3270    *
3271    * @param evt
3272    *          DOCUMENT ME!
3273    */
3274   @Override
3275   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3276   {
3277     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3278     alignPanel.paintAlignment(true, true);
3279   }
3280
3281   /**
3282    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3283    * the annotations panel as a whole.
3284    *
3285    * The options to show/hide all annotations should be enabled when the panel
3286    * is shown, and disabled when the panel is hidden.
3287    *
3288    * @param e
3289    */
3290   @Override
3291   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3292   {
3293     final boolean setVisible = annotationPanelMenuItem.isSelected();
3294     viewport.setShowAnnotation(setVisible);
3295     this.showAllSeqAnnotations.setEnabled(setVisible);
3296     this.hideAllSeqAnnotations.setEnabled(setVisible);
3297     this.showAllAlAnnotations.setEnabled(setVisible);
3298     this.hideAllAlAnnotations.setEnabled(setVisible);
3299     alignPanel.updateLayout();
3300   }
3301
3302   @Override
3303   public void alignmentProperties()
3304   {
3305     JComponent pane;
3306     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3307
3308             .formatAsHtml();
3309     String content = MessageManager.formatMessage("label.html_content",
3310             new Object[]
3311             { contents.toString() });
3312     contents = null;
3313
3314     if (Platform.isJS())
3315     {
3316       JLabel textLabel = new JLabel();
3317       textLabel.setText(content);
3318       textLabel.setBackground(Color.WHITE);
3319
3320       pane = new JPanel(new BorderLayout());
3321       ((JPanel) pane).setOpaque(true);
3322       pane.setBackground(Color.WHITE);
3323       ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3324     }
3325     else
3326     {
3327       JEditorPane editPane = new JEditorPane("text/html", "");
3328       editPane.setEditable(false);
3329       editPane.setText(content);
3330       pane = editPane;
3331     }
3332
3333     JInternalFrame frame = new JInternalFrame();
3334
3335     frame.getContentPane().add(new JScrollPane(pane));
3336
3337     Desktop.addInternalFrame(frame, MessageManager
3338             .formatMessage("label.alignment_properties", new Object[]
3339             { getTitle() }), 500, 400);
3340   }
3341
3342   /**
3343    * DOCUMENT ME!
3344    *
3345    * @param e
3346    *          DOCUMENT ME!
3347    */
3348   @Override
3349   public void overviewMenuItem_actionPerformed(ActionEvent e)
3350   {
3351     if (alignPanel.overviewPanel != null)
3352     {
3353       return;
3354     }
3355
3356     JInternalFrame frame = new JInternalFrame();
3357     final OverviewPanel overview = new OverviewPanel(alignPanel);
3358     frame.setContentPane(overview);
3359     Desktop.addInternalFrame(frame, MessageManager
3360             .formatMessage("label.overview_params", new Object[]
3361             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3362             true, true);
3363     frame.pack();
3364     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3365     frame.addInternalFrameListener(
3366             new javax.swing.event.InternalFrameAdapter()
3367             {
3368               @Override
3369               public void internalFrameClosed(
3370                       javax.swing.event.InternalFrameEvent evt)
3371               {
3372                 overview.dispose();
3373                 alignPanel.setOverviewPanel(null);
3374               }
3375             });
3376     if (getKeyListeners().length > 0)
3377     {
3378       frame.addKeyListener(getKeyListeners()[0]);
3379     }
3380
3381     alignPanel.setOverviewPanel(overview);
3382   }
3383
3384   @Override
3385   public void textColour_actionPerformed()
3386   {
3387     new TextColourChooser().chooseColour(alignPanel, null);
3388   }
3389
3390   /*
3391    * public void covariationColour_actionPerformed() {
3392    * changeColour(new
3393    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3394    * ()[0])); }
3395    */
3396   @Override
3397   public void annotationColour_actionPerformed()
3398   {
3399     new AnnotationColourChooser(viewport, alignPanel);
3400   }
3401
3402   @Override
3403   public void annotationColumn_actionPerformed(ActionEvent e)
3404   {
3405     new AnnotationColumnChooser(viewport, alignPanel);
3406   }
3407
3408   /**
3409    * Action on the user checking or unchecking the option to apply the selected
3410    * colour scheme to all groups. If unchecked, groups may have their own
3411    * independent colour schemes.
3412    *
3413    * @param selected
3414    */
3415   @Override
3416   public void applyToAllGroups_actionPerformed(boolean selected)
3417   {
3418     viewport.setColourAppliesToAllGroups(selected);
3419   }
3420
3421   /**
3422    * Action on user selecting a colour from the colour menu
3423    *
3424    * @param name
3425    *          the name (not the menu item label!) of the colour scheme
3426    */
3427   @Override
3428   public void changeColour_actionPerformed(String name)
3429   {
3430     /*
3431      * 'User Defined' opens a panel to configure or load a
3432      * user-defined colour scheme
3433      */
3434     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3435     {
3436       new UserDefinedColours(alignPanel);
3437       return;
3438     }
3439
3440     /*
3441      * otherwise set the chosen colour scheme (or null for 'None')
3442      */
3443     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3444             viewport,
3445             viewport.getAlignment(), viewport.getHiddenRepSequences());
3446     changeColour(cs);
3447   }
3448
3449   /**
3450    * Actions on setting or changing the alignment colour scheme
3451    *
3452    * @param cs
3453    */
3454   @Override
3455   public void changeColour(ColourSchemeI cs)
3456   {
3457     // TODO: pull up to controller method
3458     ColourMenuHelper.setColourSelected(colourMenu, cs);
3459
3460     viewport.setGlobalColourScheme(cs);
3461
3462     alignPanel.paintAlignment(true, true);
3463   }
3464
3465   /**
3466    * Show the PID threshold slider panel
3467    */
3468   @Override
3469   protected void modifyPID_actionPerformed()
3470   {
3471     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3472             alignPanel.getViewName());
3473     SliderPanel.showPIDSlider();
3474   }
3475
3476   /**
3477    * Show the Conservation slider panel
3478    */
3479   @Override
3480   protected void modifyConservation_actionPerformed()
3481   {
3482     SliderPanel.setConservationSlider(alignPanel,
3483             viewport.getResidueShading(), alignPanel.getViewName());
3484     SliderPanel.showConservationSlider();
3485   }
3486
3487   /**
3488    * Action on selecting or deselecting (Colour) By Conservation
3489    */
3490   @Override
3491   public void conservationMenuItem_actionPerformed(boolean selected)
3492   {
3493     modifyConservation.setEnabled(selected);
3494     viewport.setConservationSelected(selected);
3495     viewport.getResidueShading().setConservationApplied(selected);
3496
3497     changeColour(viewport.getGlobalColourScheme());
3498     if (selected)
3499     {
3500       modifyConservation_actionPerformed();
3501     }
3502     else
3503     {
3504       SliderPanel.hideConservationSlider();
3505     }
3506   }
3507
3508   /**
3509    * Action on selecting or deselecting (Colour) Above PID Threshold
3510    */
3511   @Override
3512   public void abovePIDThreshold_actionPerformed(boolean selected)
3513   {
3514     modifyPID.setEnabled(selected);
3515     viewport.setAbovePIDThreshold(selected);
3516     if (!selected)
3517     {
3518       viewport.getResidueShading().setThreshold(0,
3519               viewport.isIgnoreGapsConsensus());
3520     }
3521
3522     changeColour(viewport.getGlobalColourScheme());
3523     if (selected)
3524     {
3525       modifyPID_actionPerformed();
3526     }
3527     else
3528     {
3529       SliderPanel.hidePIDSlider();
3530     }
3531   }
3532
3533   /**
3534    * DOCUMENT ME!
3535    *
3536    * @param e
3537    *          DOCUMENT ME!
3538    */
3539   @Override
3540   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3541   {
3542     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3543     AlignmentSorter.sortByPID(viewport.getAlignment(),
3544             viewport.getAlignment().getSequenceAt(0));
3545     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3546             viewport.getAlignment()));
3547     alignPanel.paintAlignment(true, false);
3548   }
3549
3550   /**
3551    * DOCUMENT ME!
3552    *
3553    * @param e
3554    *          DOCUMENT ME!
3555    */
3556   @Override
3557   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3558   {
3559     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3560     AlignmentSorter.sortByID(viewport.getAlignment());
3561     addHistoryItem(
3562             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3563     alignPanel.paintAlignment(true, false);
3564   }
3565
3566   /**
3567    * DOCUMENT ME!
3568    *
3569    * @param e
3570    *          DOCUMENT ME!
3571    */
3572   @Override
3573   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3574   {
3575     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3576     AlignmentSorter.sortByLength(viewport.getAlignment());
3577     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3578             viewport.getAlignment()));
3579     alignPanel.paintAlignment(true, false);
3580   }
3581
3582   /**
3583    * DOCUMENT ME!
3584    *
3585    * @param e
3586    *          DOCUMENT ME!
3587    */
3588   @Override
3589   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3590   {
3591     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3592     AlignmentSorter.sortByGroup(viewport.getAlignment());
3593     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3594             viewport.getAlignment()));
3595
3596     alignPanel.paintAlignment(true, false);
3597   }
3598
3599   /**
3600    * DOCUMENT ME!
3601    *
3602    * @param e
3603    *          DOCUMENT ME!
3604    */
3605   @Override
3606   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3607   {
3608     new RedundancyPanel(alignPanel, this);
3609   }
3610
3611   /**
3612    * DOCUMENT ME!
3613    *
3614    * @param e
3615    *          DOCUMENT ME!
3616    */
3617   @Override
3618   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3619   {
3620     if ((viewport.getSelectionGroup() == null)
3621             || (viewport.getSelectionGroup().getSize() < 2))
3622     {
3623       JvOptionPane.showInternalMessageDialog(this,
3624               MessageManager.getString(
3625                       "label.you_must_select_least_two_sequences"),
3626               MessageManager.getString("label.invalid_selection"),
3627               JvOptionPane.WARNING_MESSAGE);
3628     }
3629     else
3630     {
3631       JInternalFrame frame = new JInternalFrame();
3632       frame.setContentPane(new PairwiseAlignPanel(viewport));
3633       Desktop.addInternalFrame(frame,
3634               MessageManager.getString("action.pairwise_alignment"), 600,
3635               500);
3636     }
3637   }
3638
3639   @Override
3640   public void autoCalculate_actionPerformed(ActionEvent e)
3641   {
3642     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3643     if (viewport.autoCalculateConsensus)
3644     {
3645       viewport.firePropertyChange("alignment", null,
3646               viewport.getAlignment().getSequences());
3647     }
3648   }
3649
3650   @Override
3651   public void sortByTreeOption_actionPerformed(ActionEvent e)
3652   {
3653     viewport.sortByTree = sortByTree.isSelected();
3654   }
3655
3656   @Override
3657   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3658   {
3659     viewport.followSelection = listenToViewSelections.isSelected();
3660   }
3661
3662   /**
3663    * Constructs a tree panel and adds it to the desktop
3664    *
3665    * @param type
3666    *          tree type (NJ or AV)
3667    * @param modelName
3668    *          name of score model used to compute the tree
3669    * @param options
3670    *          parameters for the distance or similarity calculation
3671    */
3672   void newTreePanel(String type, String modelName,
3673           SimilarityParamsI options)
3674   {
3675     String frameTitle = "";
3676     TreePanel tp;
3677
3678     boolean onSelection = false;
3679     if (viewport.getSelectionGroup() != null
3680             && viewport.getSelectionGroup().getSize() > 0)
3681     {
3682       SequenceGroup sg = viewport.getSelectionGroup();
3683
3684       /* Decide if the selection is a column region */
3685       for (SequenceI _s : sg.getSequences())
3686       {
3687         if (_s.getLength() < sg.getEndRes())
3688         {
3689           JvOptionPane.showMessageDialog(Desktop.desktop,
3690                   MessageManager.getString(
3691                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3692                   MessageManager.getString(
3693                           "label.sequences_selection_not_aligned"),
3694                   JvOptionPane.WARNING_MESSAGE);
3695
3696           return;
3697         }
3698       }
3699       onSelection = true;
3700     }
3701     else
3702     {
3703       if (viewport.getAlignment().getHeight() < 2)
3704       {
3705         return;
3706       }
3707     }
3708
3709     tp = new TreePanel(alignPanel, type, modelName, options);
3710     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3711
3712     frameTitle += " from ";
3713
3714     if (viewport.getViewName() != null)
3715     {
3716       frameTitle += viewport.getViewName() + " of ";
3717     }
3718
3719     frameTitle += this.title;
3720
3721     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3722   }
3723
3724   /**
3725    * DOCUMENT ME!
3726    *
3727    * @param title
3728    *          DOCUMENT ME!
3729    * @param order
3730    *          DOCUMENT ME!
3731    */
3732   public void addSortByOrderMenuItem(String title,
3733           final AlignmentOrder order)
3734   {
3735     final JMenuItem item = new JMenuItem(MessageManager
3736             .formatMessage("action.by_title_param", new Object[]
3737             { title }));
3738     sort.add(item);
3739     item.addActionListener(new java.awt.event.ActionListener()
3740     {
3741       @Override
3742       public void actionPerformed(ActionEvent e)
3743       {
3744         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3745
3746         // TODO: JBPNote - have to map order entries to curent SequenceI
3747         // pointers
3748         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3749
3750         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3751                 viewport.getAlignment()));
3752
3753         alignPanel.paintAlignment(true, false);
3754       }
3755     });
3756   }
3757
3758   /**
3759    * Add a new sort by annotation score menu item
3760    *
3761    * @param sort
3762    *          the menu to add the option to
3763    * @param scoreLabel
3764    *          the label used to retrieve scores for each sequence on the
3765    *          alignment
3766    */
3767   public void addSortByAnnotScoreMenuItem(JMenu sort,
3768           final String scoreLabel)
3769   {
3770     final JMenuItem item = new JMenuItem(scoreLabel);
3771     sort.add(item);
3772     item.addActionListener(new java.awt.event.ActionListener()
3773     {
3774       @Override
3775       public void actionPerformed(ActionEvent e)
3776       {
3777         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3778         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3779                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3780         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3781                 viewport.getAlignment()));
3782         alignPanel.paintAlignment(true, false);
3783       }
3784     });
3785   }
3786
3787   /**
3788    * last hash for alignment's annotation array - used to minimise cost of
3789    * rebuild.
3790    */
3791   protected int _annotationScoreVectorHash;
3792
3793   /**
3794    * search the alignment and rebuild the sort by annotation score submenu the
3795    * last alignment annotation vector hash is stored to minimize cost of
3796    * rebuilding in subsequence calls.
3797    *
3798    */
3799   @Override
3800   public void buildSortByAnnotationScoresMenu()
3801   {
3802     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3803     {
3804       return;
3805     }
3806
3807     if (viewport.getAlignment().getAlignmentAnnotation()
3808             .hashCode() != _annotationScoreVectorHash)
3809     {
3810       sortByAnnotScore.removeAll();
3811       // almost certainly a quicker way to do this - but we keep it simple
3812       Hashtable scoreSorts = new Hashtable();
3813       AlignmentAnnotation aann[];
3814       for (SequenceI sqa : viewport.getAlignment().getSequences())
3815       {
3816         aann = sqa.getAnnotation();
3817         for (int i = 0; aann != null && i < aann.length; i++)
3818         {
3819           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3820           {
3821             scoreSorts.put(aann[i].label, aann[i].label);
3822           }
3823         }
3824       }
3825       Enumeration labels = scoreSorts.keys();
3826       while (labels.hasMoreElements())
3827       {
3828         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3829                 (String) labels.nextElement());
3830       }
3831       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3832       scoreSorts.clear();
3833
3834       _annotationScoreVectorHash = viewport.getAlignment()
3835               .getAlignmentAnnotation().hashCode();
3836     }
3837   }
3838
3839   /**
3840    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3841    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3842    * call. Listeners are added to remove the menu item when the treePanel is
3843    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3844    * modified.
3845    */
3846   @Override
3847   public void buildTreeSortMenu()
3848   {
3849     sortByTreeMenu.removeAll();
3850
3851     List<Component> comps = PaintRefresher.components
3852             .get(viewport.getSequenceSetId());
3853     List<TreePanel> treePanels = new ArrayList<>();
3854     for (Component comp : comps)
3855     {
3856       if (comp instanceof TreePanel)
3857       {
3858         treePanels.add((TreePanel) comp);
3859       }
3860     }
3861
3862     if (treePanels.size() < 1)
3863     {
3864       sortByTreeMenu.setVisible(false);
3865       return;
3866     }
3867
3868     sortByTreeMenu.setVisible(true);
3869
3870     for (final TreePanel tp : treePanels)
3871     {
3872       final JMenuItem item = new JMenuItem(tp.getTitle());
3873       item.addActionListener(new java.awt.event.ActionListener()
3874       {
3875         @Override
3876         public void actionPerformed(ActionEvent e)
3877         {
3878           tp.sortByTree_actionPerformed();
3879           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3880
3881         }
3882       });
3883
3884       sortByTreeMenu.add(item);
3885     }
3886   }
3887
3888   public boolean sortBy(AlignmentOrder alorder, String undoname)
3889   {
3890     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3891     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3892     if (undoname != null)
3893     {
3894       addHistoryItem(new OrderCommand(undoname, oldOrder,
3895               viewport.getAlignment()));
3896     }
3897     alignPanel.paintAlignment(true, false);
3898     return true;
3899   }
3900
3901   /**
3902    * Work out whether the whole set of sequences or just the selected set will
3903    * be submitted for multiple alignment.
3904    *
3905    */
3906   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3907   {
3908     // Now, check we have enough sequences
3909     AlignmentView msa = null;
3910
3911     if ((viewport.getSelectionGroup() != null)
3912             && (viewport.getSelectionGroup().getSize() > 1))
3913     {
3914       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3915       // some common interface!
3916       /*
3917        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3918        * SequenceI[sz = seqs.getSize(false)];
3919        *
3920        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3921        * seqs.getSequenceAt(i); }
3922        */
3923       msa = viewport.getAlignmentView(true);
3924     }
3925     else if (viewport.getSelectionGroup() != null
3926             && viewport.getSelectionGroup().getSize() == 1)
3927     {
3928       int option = JvOptionPane.showConfirmDialog(this,
3929               MessageManager.getString("warn.oneseq_msainput_selection"),
3930               MessageManager.getString("label.invalid_selection"),
3931               JvOptionPane.OK_CANCEL_OPTION);
3932       if (option == JvOptionPane.OK_OPTION)
3933       {
3934         msa = viewport.getAlignmentView(false);
3935       }
3936     }
3937     else
3938     {
3939       msa = viewport.getAlignmentView(false);
3940     }
3941     return msa;
3942   }
3943
3944   /**
3945    * Decides what is submitted to a secondary structure prediction service: the
3946    * first sequence in the alignment, or in the current selection, or, if the
3947    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3948    * region or the whole alignment. (where the first sequence in the set is the
3949    * one that the prediction will be for).
3950    */
3951   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3952   {
3953     AlignmentView seqs = null;
3954
3955     if ((viewport.getSelectionGroup() != null)
3956             && (viewport.getSelectionGroup().getSize() > 0))
3957     {
3958       seqs = viewport.getAlignmentView(true);
3959     }
3960     else
3961     {
3962       seqs = viewport.getAlignmentView(false);
3963     }
3964     // limit sequences - JBPNote in future - could spawn multiple prediction
3965     // jobs
3966     // TODO: viewport.getAlignment().isAligned is a global state - the local
3967     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3968     if (!viewport.getAlignment().isAligned(false))
3969     {
3970       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3971       // TODO: if seqs.getSequences().length>1 then should really have warned
3972       // user!
3973
3974     }
3975     return seqs;
3976   }
3977
3978   /**
3979    * DOCUMENT ME!
3980    *
3981    * @param e
3982    *          DOCUMENT ME!
3983    */
3984   @Override
3985   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3986   {
3987     // Pick the tree file
3988     JalviewFileChooser chooser = new JalviewFileChooser(
3989             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3990     chooser.setFileView(new JalviewFileView());
3991     chooser.setDialogTitle(
3992             MessageManager.getString("label.select_newick_like_tree_file"));
3993     chooser.setToolTipText(
3994             MessageManager.getString("label.load_tree_file"));
3995
3996     chooser.setResponseHandler(0,new Runnable()
3997     {
3998       @Override
3999       public void run()
4000       {
4001         String filePath = chooser.getSelectedFile().getPath();
4002         Cache.setProperty("LAST_DIRECTORY", filePath);
4003         NewickFile fin = null;
4004         try
4005         {
4006           fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
4007                   DataSourceType.FILE));
4008           viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4009         } catch (Exception ex)
4010         {
4011           JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4012                   MessageManager
4013                           .getString("label.problem_reading_tree_file"),
4014                   JvOptionPane.WARNING_MESSAGE);
4015           ex.printStackTrace();
4016         }
4017         if (fin != null && fin.hasWarningMessage())
4018         {
4019           JvOptionPane.showMessageDialog(Desktop.desktop,
4020                   fin.getWarningMessage(),
4021                   MessageManager.getString(
4022                           "label.possible_problem_with_tree_file"),
4023                   JvOptionPane.WARNING_MESSAGE);
4024         }
4025       }
4026     });
4027     chooser.showOpenDialog(this);
4028   }
4029
4030   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4031   {
4032     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4033   }
4034
4035   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4036           int h, int x, int y)
4037   {
4038     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4039   }
4040
4041   /**
4042    * Add a treeviewer for the tree extracted from a Newick file object to the
4043    * current alignment view
4044    *
4045    * @param nf
4046    *          the tree
4047    * @param title
4048    *          tree viewer title
4049    * @param input
4050    *          Associated alignment input data (or null)
4051    * @param w
4052    *          width
4053    * @param h
4054    *          height
4055    * @param x
4056    *          position
4057    * @param y
4058    *          position
4059    * @return TreePanel handle
4060    */
4061   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4062           AlignmentView input, int w, int h, int x, int y)
4063   {
4064     TreePanel tp = null;
4065
4066     try
4067     {
4068       nf.parse();
4069
4070       if (nf.getTree() != null)
4071       {
4072         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4073
4074         tp.setSize(w, h);
4075
4076         if (x > 0 && y > 0)
4077         {
4078           tp.setLocation(x, y);
4079         }
4080
4081         Desktop.addInternalFrame(tp, treeTitle, w, h);
4082       }
4083     } catch (Exception ex)
4084     {
4085       ex.printStackTrace();
4086     }
4087
4088     return tp;
4089   }
4090
4091   private boolean buildingMenu = false;
4092
4093   /**
4094    * Generates menu items and listener event actions for web service clients
4095    *
4096    */
4097   public void BuildWebServiceMenu()
4098   {
4099     while (buildingMenu)
4100     {
4101       try
4102       {
4103         System.err.println("Waiting for building menu to finish.");
4104         Thread.sleep(10);
4105       } catch (Exception e)
4106       {
4107       }
4108     }
4109     final AlignFrame me = this;
4110     buildingMenu = true;
4111     new Thread(new Runnable()
4112     {
4113       @Override
4114       public void run()
4115       {
4116         final List<JMenuItem> legacyItems = new ArrayList<>();
4117         try
4118         {
4119           // System.err.println("Building ws menu again "
4120           // + Thread.currentThread());
4121           // TODO: add support for context dependent disabling of services based
4122           // on
4123           // alignment and current selection
4124           // TODO: add additional serviceHandle parameter to specify abstract
4125           // handler
4126           // class independently of AbstractName
4127           // TODO: add in rediscovery GUI function to restart discoverer
4128           // TODO: group services by location as well as function and/or
4129           // introduce
4130           // object broker mechanism.
4131           final Vector<JMenu> wsmenu = new Vector<>();
4132           final IProgressIndicator af = me;
4133
4134           /*
4135            * do not i18n these strings - they are hard-coded in class
4136            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4137            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4138            */
4139           final JMenu msawsmenu = new JMenu("Alignment");
4140           final JMenu secstrmenu = new JMenu(
4141                   "Secondary Structure Prediction");
4142           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4143           final JMenu analymenu = new JMenu("Analysis");
4144           final JMenu dismenu = new JMenu("Protein Disorder");
4145           // JAL-940 - only show secondary structure prediction services from
4146           // the legacy server
4147           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4148               // &&
4149           Discoverer.services != null && (Discoverer.services.size() > 0))
4150           {
4151             // TODO: refactor to allow list of AbstractName/Handler bindings to
4152             // be
4153             // stored or retrieved from elsewhere
4154             // No MSAWS used any more:
4155             // Vector msaws = null; // (Vector)
4156             // Discoverer.services.get("MsaWS");
4157             Vector secstrpr = (Vector) Discoverer.services
4158                     .get("SecStrPred");
4159             if (secstrpr != null)
4160             {
4161               // Add any secondary structure prediction services
4162               for (int i = 0, j = secstrpr.size(); i < j; i++)
4163               {
4164                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4165                         .get(i);
4166                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4167                         .getServiceClient(sh);
4168                 int p = secstrmenu.getItemCount();
4169                 impl.attachWSMenuEntry(secstrmenu, me);
4170                 int q = secstrmenu.getItemCount();
4171                 for (int litm = p; litm < q; litm++)
4172                 {
4173                   legacyItems.add(secstrmenu.getItem(litm));
4174                 }
4175               }
4176             }
4177           }
4178
4179           // Add all submenus in the order they should appear on the web
4180           // services menu
4181           wsmenu.add(msawsmenu);
4182           wsmenu.add(secstrmenu);
4183           wsmenu.add(dismenu);
4184           wsmenu.add(analymenu);
4185           // No search services yet
4186           // wsmenu.add(seqsrchmenu);
4187
4188           javax.swing.SwingUtilities.invokeLater(new Runnable()
4189           {
4190             @Override
4191             public void run()
4192             {
4193               try
4194               {
4195                 webService.removeAll();
4196                 // first, add discovered services onto the webservices menu
4197                 if (wsmenu.size() > 0)
4198                 {
4199                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4200                   {
4201                     webService.add(wsmenu.get(i));
4202                   }
4203                 }
4204                 else
4205                 {
4206                   webService.add(me.webServiceNoServices);
4207                 }
4208                 // TODO: move into separate menu builder class.
4209                 boolean new_sspred = false;
4210                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4211                 {
4212                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4213                   if (jws2servs != null)
4214                   {
4215                     if (jws2servs.hasServices())
4216                     {
4217                       jws2servs.attachWSMenuEntry(webService, me);
4218                       for (Jws2Instance sv : jws2servs.getServices())
4219                       {
4220                         if (sv.description.toLowerCase().contains("jpred"))
4221                         {
4222                           for (JMenuItem jmi : legacyItems)
4223                           {
4224                             jmi.setVisible(false);
4225                           }
4226                         }
4227                       }
4228
4229                     }
4230                     if (jws2servs.isRunning())
4231                     {
4232                       JMenuItem tm = new JMenuItem(
4233                               "Still discovering JABA Services");
4234                       tm.setEnabled(false);
4235                       webService.add(tm);
4236                     }
4237                   }
4238                 }
4239                 build_urlServiceMenu(me.webService);
4240                 build_fetchdbmenu(webService);
4241                 for (JMenu item : wsmenu)
4242                 {
4243                   if (item.getItemCount() == 0)
4244                   {
4245                     item.setEnabled(false);
4246                   }
4247                   else
4248                   {
4249                     item.setEnabled(true);
4250                   }
4251                 }
4252               } catch (Exception e)
4253               {
4254                 Cache.log.debug(
4255                         "Exception during web service menu building process.",
4256                         e);
4257               }
4258             }
4259           });
4260         } catch (Exception e)
4261         {
4262         }
4263         buildingMenu = false;
4264       }
4265     }).start();
4266
4267   }
4268
4269   /**
4270    * construct any groupURL type service menu entries.
4271    *
4272    * @param webService
4273    */
4274   private void build_urlServiceMenu(JMenu webService)
4275   {
4276     // TODO: remove this code when 2.7 is released
4277     // DEBUG - alignmentView
4278     /*
4279      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4280      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4281      *
4282      * @Override public void actionPerformed(ActionEvent e) {
4283      * jalview.datamodel.AlignmentView
4284      * .testSelectionViews(af.viewport.getAlignment(),
4285      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4286      *
4287      * }); webService.add(testAlView);
4288      */
4289     // TODO: refactor to RestClient discoverer and merge menu entries for
4290     // rest-style services with other types of analysis/calculation service
4291     // SHmmr test client - still being implemented.
4292     // DEBUG - alignmentView
4293
4294     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4295             .getRestClients())
4296     {
4297       client.attachWSMenuEntry(
4298               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4299               this);
4300     }
4301   }
4302
4303   /**
4304    * Searches the alignment sequences for xRefs and builds the Show
4305    * Cross-References menu (formerly called Show Products), with database
4306    * sources for which cross-references are found (protein sources for a
4307    * nucleotide alignment and vice versa)
4308    *
4309    * @return true if Show Cross-references menu should be enabled
4310    */
4311   public boolean canShowProducts()
4312   {
4313     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4314     AlignmentI dataset = viewport.getAlignment().getDataset();
4315
4316     showProducts.removeAll();
4317     final boolean dna = viewport.getAlignment().isNucleotide();
4318
4319     if (seqs == null || seqs.length == 0)
4320     {
4321       // nothing to see here.
4322       return false;
4323     }
4324
4325     boolean showp = false;
4326     try
4327     {
4328       List<String> ptypes = new CrossRef(seqs, dataset)
4329               .findXrefSourcesForSequences(dna);
4330
4331       for (final String source : ptypes)
4332       {
4333         showp = true;
4334         final AlignFrame af = this;
4335         JMenuItem xtype = new JMenuItem(source);
4336         xtype.addActionListener(new ActionListener()
4337         {
4338           @Override
4339           public void actionPerformed(ActionEvent e)
4340           {
4341             showProductsFor(af.viewport.getSequenceSelection(), dna,
4342                     source);
4343           }
4344         });
4345         showProducts.add(xtype);
4346       }
4347       showProducts.setVisible(showp);
4348       showProducts.setEnabled(showp);
4349     } catch (Exception e)
4350     {
4351       Cache.log.warn(
4352               "canShowProducts threw an exception - please report to help@jalview.org",
4353               e);
4354       return false;
4355     }
4356     return showp;
4357   }
4358
4359   /**
4360    * Finds and displays cross-references for the selected sequences (protein
4361    * products for nucleotide sequences, dna coding sequences for peptides).
4362    *
4363    * @param sel
4364    *          the sequences to show cross-references for
4365    * @param dna
4366    *          true if from a nucleotide alignment (so showing proteins)
4367    * @param source
4368    *          the database to show cross-references for
4369    */
4370   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4371           final String source)
4372   {
4373     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4374             .start();
4375   }
4376
4377   /**
4378    * Construct and display a new frame containing the translation of this
4379    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4380    */
4381   @Override
4382   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4383   {
4384     AlignmentI al = null;
4385     try
4386     {
4387       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4388
4389       al = dna.translateCdna(codeTable);
4390     } catch (Exception ex)
4391     {
4392       jalview.bin.Cache.log.error(
4393               "Exception during translation. Please report this !", ex);
4394       final String msg = MessageManager.getString(
4395               "label.error_when_translating_sequences_submit_bug_report");
4396       final String errorTitle = MessageManager
4397               .getString("label.implementation_error")
4398               + MessageManager.getString("label.translation_failed");
4399       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4400               JvOptionPane.ERROR_MESSAGE);
4401       return;
4402     }
4403     if (al == null || al.getHeight() == 0)
4404     {
4405       final String msg = MessageManager.getString(
4406               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4407       final String errorTitle = MessageManager
4408               .getString("label.translation_failed");
4409       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4410               JvOptionPane.WARNING_MESSAGE);
4411     }
4412     else
4413     {
4414       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4415       af.setFileFormat(this.currentFileFormat);
4416       final String newTitle = MessageManager
4417               .formatMessage("label.translation_of_params", new Object[]
4418               { this.getTitle(), codeTable.getId() });
4419       af.setTitle(newTitle);
4420       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4421       {
4422         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4423         viewport.openSplitFrame(af, new Alignment(seqs));
4424       }
4425       else
4426       {
4427         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4428                 DEFAULT_HEIGHT);
4429       }
4430     }
4431   }
4432
4433   /**
4434    * Set the file format
4435    *
4436    * @param format
4437    */
4438   public void setFileFormat(FileFormatI format)
4439   {
4440     this.currentFileFormat = format;
4441   }
4442
4443   /**
4444    * Try to load a features file onto the alignment.
4445    *
4446    * @param file
4447    *          contents or path to retrieve file or a File object
4448    * @param sourceType
4449    *          access mode of file (see jalview.io.AlignFile)
4450    * @return true if features file was parsed correctly.
4451    */
4452   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4453   {
4454     // BH 2018
4455     return avc.parseFeaturesFile(file, sourceType,
4456             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4457
4458   }
4459
4460   @Override
4461   public void refreshFeatureUI(boolean enableIfNecessary)
4462   {
4463     // note - currently this is only still here rather than in the controller
4464     // because of the featureSettings hard reference that is yet to be
4465     // abstracted
4466     if (enableIfNecessary)
4467     {
4468       viewport.setShowSequenceFeatures(true);
4469       showSeqFeatures.setSelected(true);
4470     }
4471
4472   }
4473
4474   @Override
4475   public void dragEnter(DropTargetDragEvent evt)
4476   {
4477   }
4478
4479   @Override
4480   public void dragExit(DropTargetEvent evt)
4481   {
4482   }
4483
4484   @Override
4485   public void dragOver(DropTargetDragEvent evt)
4486   {
4487   }
4488
4489   @Override
4490   public void dropActionChanged(DropTargetDragEvent evt)
4491   {
4492   }
4493
4494   @Override
4495   public void drop(DropTargetDropEvent evt)
4496   {
4497     // JAL-1552 - acceptDrop required before getTransferable call for
4498     // Java's Transferable for native dnd
4499     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4500     Transferable t = evt.getTransferable();
4501
4502     final AlignFrame thisaf = this;
4503     final List<Object> files = new ArrayList<>();
4504     List<DataSourceType> protocols = new ArrayList<>();
4505
4506     try
4507     {
4508       Desktop.transferFromDropTarget(files, protocols, evt, t);
4509     } catch (Exception e)
4510     {
4511       e.printStackTrace();
4512     }
4513     if (files != null)
4514     {
4515       new Thread(new Runnable()
4516       {
4517         @Override
4518         public void run()
4519         {
4520           try
4521           {
4522             // check to see if any of these files have names matching sequences
4523             // in
4524             // the alignment
4525             SequenceIdMatcher idm = new SequenceIdMatcher(
4526                     viewport.getAlignment().getSequencesArray());
4527             /**
4528              * Object[] { String,SequenceI}
4529              */
4530             ArrayList<Object[]> filesmatched = new ArrayList<>();
4531             ArrayList<Object> filesnotmatched = new ArrayList<>();
4532             for (int i = 0; i < files.size(); i++)
4533             {
4534               // BH 2018
4535               Object file = files.get(i);
4536               String fileName = file.toString();
4537               String pdbfn = "";
4538               DataSourceType protocol = (file instanceof File
4539                       ? DataSourceType.FILE
4540                       : FormatAdapter.checkProtocol(fileName));
4541               if (protocol == DataSourceType.FILE)
4542               {
4543                 File fl = (file instanceof File ? (File) file
4544                         : new File(fileName));
4545                 pdbfn = fl.getName();
4546               }
4547               else if (protocol == DataSourceType.URL)
4548               {
4549                 URL url = new URL(fileName);
4550                 pdbfn = url.getFile();
4551               }
4552               if (pdbfn.length() > 0)
4553               {
4554                 // attempt to find a match in the alignment
4555                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4556                 int l = 0, c = pdbfn.indexOf(".");
4557                 while (mtch == null && c != -1)
4558                 {
4559                   do
4560                   {
4561                     l = c;
4562                   } while ((c = pdbfn.indexOf(".", l)) > l);
4563                   if (l > -1)
4564                   {
4565                     pdbfn = pdbfn.substring(0, l);
4566                   }
4567                   mtch = idm.findAllIdMatches(pdbfn);
4568                 }
4569                 if (mtch != null)
4570                 {
4571                   FileFormatI type;
4572                   try
4573                   {
4574                     type = new IdentifyFile().identify(file, protocol);
4575                   } catch (Exception ex)
4576                   {
4577                     type = null;
4578                   }
4579                   if (type != null && type.isStructureFile())
4580                   {
4581                     filesmatched.add(new Object[] { file, protocol, mtch });
4582                     continue;
4583                   }
4584                 }
4585                 // File wasn't named like one of the sequences or wasn't a PDB
4586                 // file.
4587                 filesnotmatched.add(file);
4588               }
4589             }
4590             int assocfiles = 0;
4591             if (filesmatched.size() > 0)
4592             {
4593               boolean autoAssociate = Cache
4594                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4595               if (!autoAssociate)
4596               {
4597                 String msg = MessageManager.formatMessage(
4598                         "label.automatically_associate_structure_files_with_sequences_same_name",
4599                         new Object[]
4600                         { Integer.valueOf(filesmatched.size())
4601                                 .toString() });
4602                 String ttl = MessageManager.getString(
4603                         "label.automatically_associate_structure_files_by_name");
4604                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4605                         ttl, JvOptionPane.YES_NO_OPTION);
4606                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4607               }
4608               if (autoAssociate)
4609               {
4610                 for (Object[] fm : filesmatched)
4611                 {
4612                   // try and associate
4613                   // TODO: may want to set a standard ID naming formalism for
4614                   // associating PDB files which have no IDs.
4615                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4616                   {
4617                     PDBEntry pe = new AssociatePdbFileWithSeq()
4618                             .associatePdbWithSeq(fm[0].toString(),
4619                                     (DataSourceType) fm[1], toassoc, false,
4620                                     Desktop.instance);
4621                     if (pe != null)
4622                     {
4623                       System.err.println("Associated file : "
4624                               + (fm[0].toString()) + " with "
4625                               + toassoc.getDisplayId(true));
4626                       assocfiles++;
4627                     }
4628                   }
4629                   // TODO: do we need to update overview ? only if features are
4630                   // shown I guess
4631                   alignPanel.paintAlignment(true, false);
4632                 }
4633               }
4634               else
4635               {
4636                 /*
4637                  * add declined structures as sequences
4638                  */
4639                 for (Object[] o : filesmatched)
4640                 {
4641                   filesnotmatched.add(o[0]);
4642                 }
4643               }
4644             }
4645             if (filesnotmatched.size() > 0)
4646             {
4647               if (assocfiles > 0 && (Cache.getDefault(
4648                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4649                       || JvOptionPane.showConfirmDialog(thisaf,
4650                               "<html>" + MessageManager.formatMessage(
4651                                       "label.ignore_unmatched_dropped_files_info",
4652                                       new Object[]
4653                                       { Integer.valueOf(
4654                                               filesnotmatched.size())
4655                                               .toString() })
4656                                       + "</html>",
4657                               MessageManager.getString(
4658                                       "label.ignore_unmatched_dropped_files"),
4659                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4660               {
4661                 return;
4662               }
4663               for (Object fn : filesnotmatched)
4664               {
4665                 loadJalviewDataFile(fn, null, null, null);
4666               }
4667
4668             }
4669           } catch (Exception ex)
4670           {
4671             ex.printStackTrace();
4672           }
4673         }
4674       }).start();
4675     }
4676   }
4677
4678   /**
4679    * Attempt to load a "dropped" file or URL string, by testing in turn for
4680    * <ul>
4681    * <li>an Annotation file</li>
4682    * <li>a JNet file</li>
4683    * <li>a features file</li>
4684    * <li>else try to interpret as an alignment file</li>
4685    * </ul>
4686    *
4687    * @param file
4688    *          either a filename or a URL string.
4689    */
4690   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4691           FileFormatI format, SequenceI assocSeq)
4692   {
4693     // BH 2018 was String file
4694     try
4695     {
4696       if (sourceType == null)
4697       {
4698         sourceType = FormatAdapter.checkProtocol(file);
4699       }
4700       // if the file isn't identified, or not positively identified as some
4701       // other filetype (PFAM is default unidentified alignment file type) then
4702       // try to parse as annotation.
4703       boolean isAnnotation = (format == null
4704               || FileFormat.Pfam.equals(format))
4705                       ? new AnnotationFile().annotateAlignmentView(viewport,
4706                               file, sourceType)
4707                       : false;
4708
4709       if (!isAnnotation)
4710       {
4711         // first see if its a T-COFFEE score file
4712         TCoffeeScoreFile tcf = null;
4713         try
4714         {
4715           tcf = new TCoffeeScoreFile(file, sourceType);
4716           if (tcf.isValid())
4717           {
4718             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4719             {
4720               buildColourMenu();
4721               changeColour(
4722                       new TCoffeeColourScheme(viewport.getAlignment()));
4723               isAnnotation = true;
4724               setStatus(MessageManager.getString(
4725                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4726             }
4727             else
4728             {
4729               // some problem - if no warning its probable that the ID matching
4730               // process didn't work
4731               JvOptionPane.showMessageDialog(Desktop.desktop,
4732                       tcf.getWarningMessage() == null
4733                               ? MessageManager.getString(
4734                                       "label.check_file_matches_sequence_ids_alignment")
4735                               : tcf.getWarningMessage(),
4736                       MessageManager.getString(
4737                               "label.problem_reading_tcoffee_score_file"),
4738                       JvOptionPane.WARNING_MESSAGE);
4739             }
4740           }
4741           else
4742           {
4743             tcf = null;
4744           }
4745         } catch (Exception x)
4746         {
4747           Cache.log.debug(
4748                   "Exception when processing data source as T-COFFEE score file",
4749                   x);
4750           tcf = null;
4751         }
4752         if (tcf == null)
4753         {
4754           // try to see if its a JNet 'concise' style annotation file *before*
4755           // we
4756           // try to parse it as a features file
4757           if (format == null)
4758           {
4759             format = new IdentifyFile().identify(file, sourceType);
4760           }
4761           if (FileFormat.ScoreMatrix == format)
4762           {
4763             ScoreMatrixFile sm = new ScoreMatrixFile(
4764                     new FileParse(file, sourceType));
4765             sm.parse();
4766             // todo: i18n this message
4767             setStatus(MessageManager.formatMessage(
4768                     "label.successfully_loaded_matrix",
4769                     sm.getMatrixName()));
4770           }
4771           else if (FileFormat.Jnet.equals(format))
4772           {
4773             JPredFile predictions = new JPredFile(file, sourceType);
4774             new JnetAnnotationMaker();
4775             JnetAnnotationMaker.add_annotation(predictions,
4776                     viewport.getAlignment(), 0, false);
4777             viewport.getAlignment().setupJPredAlignment();
4778             isAnnotation = true;
4779           }
4780           // else if (IdentifyFile.FeaturesFile.equals(format))
4781           else if (FileFormat.Features.equals(format))
4782           {
4783             if (parseFeaturesFile(file, sourceType))
4784             {
4785               alignPanel.paintAlignment(true, true);
4786             }
4787           }
4788           else
4789           {
4790             new FileLoader().LoadFile(viewport, file, sourceType, format);
4791           }
4792         }
4793       }
4794       if (isAnnotation)
4795       {
4796
4797         alignPanel.adjustAnnotationHeight();
4798         viewport.updateSequenceIdColours();
4799         buildSortByAnnotationScoresMenu();
4800         alignPanel.paintAlignment(true, true);
4801       }
4802     } catch (Exception ex)
4803     {
4804       ex.printStackTrace();
4805     } catch (OutOfMemoryError oom)
4806     {
4807       try
4808       {
4809         System.gc();
4810       } catch (Exception x)
4811       {
4812       }
4813       new OOMWarning(
4814               "loading data "
4815                       + (sourceType != null
4816                               ? (sourceType == DataSourceType.PASTE
4817                                       ? "from clipboard."
4818                                       : "using " + sourceType + " from "
4819                                               + file)
4820                               : ".")
4821                       + (format != null
4822                               ? "(parsing as '" + format + "' file)"
4823                               : ""),
4824               oom, Desktop.desktop);
4825     }
4826   }
4827
4828   /**
4829    * Method invoked by the ChangeListener on the tabbed pane, in other words
4830    * when a different tabbed pane is selected by the user or programmatically.
4831    */
4832   @Override
4833   public void tabSelectionChanged(int index)
4834   {
4835     if (index > -1)
4836     {
4837       alignPanel = alignPanels.get(index);
4838       viewport = alignPanel.av;
4839       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4840       setMenusFromViewport(viewport);
4841     }
4842
4843     /*
4844      * 'focus' any colour slider that is open to the selected viewport
4845      */
4846     if (viewport.getConservationSelected())
4847     {
4848       SliderPanel.setConservationSlider(alignPanel,
4849               viewport.getResidueShading(), alignPanel.getViewName());
4850     }
4851     else
4852     {
4853       SliderPanel.hideConservationSlider();
4854     }
4855     if (viewport.getAbovePIDThreshold())
4856     {
4857       SliderPanel.setPIDSliderSource(alignPanel,
4858               viewport.getResidueShading(), alignPanel.getViewName());
4859     }
4860     else
4861     {
4862       SliderPanel.hidePIDSlider();
4863     }
4864
4865     /*
4866      * If there is a frame linked to this one in a SplitPane, switch it to the
4867      * same view tab index. No infinite recursion of calls should happen, since
4868      * tabSelectionChanged() should not get invoked on setting the selected
4869      * index to an unchanged value. Guard against setting an invalid index
4870      * before the new view peer tab has been created.
4871      */
4872     final AlignViewportI peer = viewport.getCodingComplement();
4873     if (peer != null)
4874     {
4875       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4876               .getAlignPanel().alignFrame;
4877       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4878       {
4879         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4880       }
4881     }
4882   }
4883
4884   /**
4885    * On right mouse click on view tab, prompt for and set new view name.
4886    */
4887   @Override
4888   public void tabbedPane_mousePressed(MouseEvent e)
4889   {
4890     if (e.isPopupTrigger())
4891     {
4892       String msg = MessageManager.getString("label.enter_view_name");
4893       String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
4894       String reply = JvOptionPane.showInputDialog(msg, ttl);
4895
4896       if (reply != null)
4897       {
4898         viewport.setViewName(reply);
4899         // TODO warn if reply is in getExistingViewNames()?
4900         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4901       }
4902     }
4903   }
4904
4905   public AlignViewport getCurrentView()
4906   {
4907     return viewport;
4908   }
4909
4910   /**
4911    * Open the dialog for regex description parsing.
4912    */
4913   @Override
4914   protected void extractScores_actionPerformed(ActionEvent e)
4915   {
4916     ParseProperties pp = new jalview.analysis.ParseProperties(
4917             viewport.getAlignment());
4918     // TODO: verify regex and introduce GUI dialog for version 2.5
4919     // if (pp.getScoresFromDescription("col", "score column ",
4920     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4921     // true)>0)
4922     if (pp.getScoresFromDescription("description column",
4923             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4924     {
4925       buildSortByAnnotationScoresMenu();
4926     }
4927   }
4928
4929   /*
4930    * (non-Javadoc)
4931    *
4932    * @see
4933    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4934    * )
4935    */
4936   @Override
4937   protected void showDbRefs_actionPerformed(ActionEvent e)
4938   {
4939     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4940   }
4941
4942   /*
4943    * (non-Javadoc)
4944    *
4945    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4946    * ActionEvent)
4947    */
4948   @Override
4949   protected void showNpFeats_actionPerformed(ActionEvent e)
4950   {
4951     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4952   }
4953
4954   /**
4955    * find the viewport amongst the tabs in this alignment frame and close that
4956    * tab
4957    *
4958    * @param av
4959    */
4960   public boolean closeView(AlignViewportI av)
4961   {
4962     if (viewport == av)
4963     {
4964       this.closeMenuItem_actionPerformed(false);
4965       return true;
4966     }
4967     Component[] comp = tabbedPane.getComponents();
4968     for (int i = 0; comp != null && i < comp.length; i++)
4969     {
4970       if (comp[i] instanceof AlignmentPanel)
4971       {
4972         if (((AlignmentPanel) comp[i]).av == av)
4973         {
4974           // close the view.
4975           closeView((AlignmentPanel) comp[i]);
4976           return true;
4977         }
4978       }
4979     }
4980     return false;
4981   }
4982
4983   protected void build_fetchdbmenu(JMenu webService)
4984   {
4985     // Temporary hack - DBRef Fetcher always top level ws entry.
4986     // TODO We probably want to store a sequence database checklist in
4987     // preferences and have checkboxes.. rather than individual sources selected
4988     // here
4989     final JMenu rfetch = new JMenu(
4990             MessageManager.getString("action.fetch_db_references"));
4991     rfetch.setToolTipText(MessageManager.getString(
4992             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4993     webService.add(rfetch);
4994
4995     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4996             MessageManager.getString("option.trim_retrieved_seqs"));
4997     trimrs.setToolTipText(
4998             MessageManager.getString("label.trim_retrieved_sequences"));
4999     trimrs.setSelected(
5000             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5001     trimrs.addActionListener(new ActionListener()
5002     {
5003       @Override
5004       public void actionPerformed(ActionEvent e)
5005       {
5006         trimrs.setSelected(trimrs.isSelected());
5007         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5008                 Boolean.valueOf(trimrs.isSelected()).toString());
5009       }
5010     });
5011     rfetch.add(trimrs);
5012     JMenuItem fetchr = new JMenuItem(
5013             MessageManager.getString("label.standard_databases"));
5014     fetchr.setToolTipText(
5015             MessageManager.getString("label.fetch_embl_uniprot"));
5016     fetchr.addActionListener(new ActionListener()
5017     {
5018
5019       @Override
5020       public void actionPerformed(ActionEvent e)
5021       {
5022         new Thread(new Runnable()
5023         {
5024           @Override
5025           public void run()
5026           {
5027             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5028                     .getAlignment().isNucleotide();
5029             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5030                     alignPanel.av.getSequenceSelection(),
5031                     alignPanel.alignFrame, null,
5032                     alignPanel.alignFrame.featureSettings, isNucleotide);
5033             dbRefFetcher.addListener(new FetchFinishedListenerI()
5034             {
5035               @Override
5036               public void finished()
5037               {
5038                 AlignFrame.this.setMenusForViewport();
5039               }
5040             });
5041             dbRefFetcher.fetchDBRefs(false);
5042           }
5043         }).start();
5044
5045       }
5046
5047     });
5048     rfetch.add(fetchr);
5049     new Thread(new Runnable()
5050     {
5051       @Override
5052       public void run()
5053       {
5054         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5055                 .getSequenceFetcherSingleton();
5056         javax.swing.SwingUtilities.invokeLater(new Runnable()
5057         {
5058           @Override
5059           public void run()
5060           {
5061             String[] dbclasses = sf.getNonAlignmentSources();
5062             List<DbSourceProxy> otherdb;
5063             JMenu dfetch = new JMenu();
5064             JMenu ifetch = new JMenu();
5065             JMenuItem fetchr = null;
5066             int comp = 0, icomp = 0, mcomp = 15;
5067             String mname = null;
5068             int dbi = 0;
5069             for (String dbclass : dbclasses)
5070             {
5071               otherdb = sf.getSourceProxy(dbclass);
5072               // add a single entry for this class, or submenu allowing 'fetch
5073               // all' or pick one
5074               if (otherdb == null || otherdb.size() < 1)
5075               {
5076                 continue;
5077               }
5078               if (mname == null)
5079               {
5080                 mname = "From " + dbclass;
5081               }
5082               if (otherdb.size() == 1)
5083               {
5084                 final DbSourceProxy[] dassource = otherdb
5085                         .toArray(new DbSourceProxy[0]);
5086                 DbSourceProxy src = otherdb.get(0);
5087                 fetchr = new JMenuItem(src.getDbSource());
5088                 fetchr.addActionListener(new ActionListener()
5089                 {
5090
5091                   @Override
5092                   public void actionPerformed(ActionEvent e)
5093                   {
5094                     new Thread(new Runnable()
5095                     {
5096
5097                       @Override
5098                       public void run()
5099                       {
5100                         boolean isNucleotide = alignPanel.alignFrame
5101                                 .getViewport().getAlignment()
5102                                 .isNucleotide();
5103                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5104                                 alignPanel.av.getSequenceSelection(),
5105                                 alignPanel.alignFrame, dassource,
5106                                 alignPanel.alignFrame.featureSettings,
5107                                 isNucleotide);
5108                         dbRefFetcher
5109                                 .addListener(new FetchFinishedListenerI()
5110                                 {
5111                                   @Override
5112                                   public void finished()
5113                                   {
5114                                     AlignFrame.this.setMenusForViewport();
5115                                   }
5116                                 });
5117                         dbRefFetcher.fetchDBRefs(false);
5118                       }
5119                     }).start();
5120                   }
5121
5122                 });
5123                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5124                         MessageManager.formatMessage(
5125                                 "label.fetch_retrieve_from", new Object[]
5126                                 { src.getDbName() })));
5127                 dfetch.add(fetchr);
5128                 comp++;
5129               }
5130               else
5131               {
5132                 final DbSourceProxy[] dassource = otherdb
5133                         .toArray(new DbSourceProxy[0]);
5134                 // fetch all entry
5135                 DbSourceProxy src = otherdb.get(0);
5136                 fetchr = new JMenuItem(MessageManager
5137                         .formatMessage("label.fetch_all_param", new Object[]
5138                         { src.getDbSource() }));
5139                 fetchr.addActionListener(new ActionListener()
5140                 {
5141                   @Override
5142                   public void actionPerformed(ActionEvent e)
5143                   {
5144                     new Thread(new Runnable()
5145                     {
5146
5147                       @Override
5148                       public void run()
5149                       {
5150                         boolean isNucleotide = alignPanel.alignFrame
5151                                 .getViewport().getAlignment()
5152                                 .isNucleotide();
5153                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5154                                 alignPanel.av.getSequenceSelection(),
5155                                 alignPanel.alignFrame, dassource,
5156                                 alignPanel.alignFrame.featureSettings,
5157                                 isNucleotide);
5158                         dbRefFetcher
5159                                 .addListener(new FetchFinishedListenerI()
5160                                 {
5161                                   @Override
5162                                   public void finished()
5163                                   {
5164                                     AlignFrame.this.setMenusForViewport();
5165                                   }
5166                                 });
5167                         dbRefFetcher.fetchDBRefs(false);
5168                       }
5169                     }).start();
5170                   }
5171                 });
5172
5173                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5174                         MessageManager.formatMessage(
5175                                 "label.fetch_retrieve_from_all_sources",
5176                                 new Object[]
5177                                 { Integer.valueOf(otherdb.size())
5178                                         .toString(),
5179                                     src.getDbSource(), src.getDbName() })));
5180                 dfetch.add(fetchr);
5181                 comp++;
5182                 // and then build the rest of the individual menus
5183                 ifetch = new JMenu(MessageManager.formatMessage(
5184                         "label.source_from_db_source", new Object[]
5185                         { src.getDbSource() }));
5186                 icomp = 0;
5187                 String imname = null;
5188                 int i = 0;
5189                 for (DbSourceProxy sproxy : otherdb)
5190                 {
5191                   String dbname = sproxy.getDbName();
5192                   String sname = dbname.length() > 5
5193                           ? dbname.substring(0, 5) + "..."
5194                           : dbname;
5195                   String msname = dbname.length() > 10
5196                           ? dbname.substring(0, 10) + "..."
5197                           : dbname;
5198                   if (imname == null)
5199                   {
5200                     imname = MessageManager
5201                             .formatMessage("label.from_msname", new Object[]
5202                             { sname });
5203                   }
5204                   fetchr = new JMenuItem(msname);
5205                   final DbSourceProxy[] dassrc = { sproxy };
5206                   fetchr.addActionListener(new ActionListener()
5207                   {
5208
5209                     @Override
5210                     public void actionPerformed(ActionEvent e)
5211                     {
5212                       new Thread(new Runnable()
5213                       {
5214
5215                         @Override
5216                         public void run()
5217                         {
5218                           boolean isNucleotide = alignPanel.alignFrame
5219                                   .getViewport().getAlignment()
5220                                   .isNucleotide();
5221                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5222                                   alignPanel.av.getSequenceSelection(),
5223                                   alignPanel.alignFrame, dassrc,
5224                                   alignPanel.alignFrame.featureSettings,
5225                                   isNucleotide);
5226                           dbRefFetcher
5227                                   .addListener(new FetchFinishedListenerI()
5228                                   {
5229                                     @Override
5230                                     public void finished()
5231                                     {
5232                                       AlignFrame.this.setMenusForViewport();
5233                                     }
5234                                   });
5235                           dbRefFetcher.fetchDBRefs(false);
5236                         }
5237                       }).start();
5238                     }
5239
5240                   });
5241                   fetchr.setToolTipText(
5242                           "<html>" + MessageManager.formatMessage(
5243                                   "label.fetch_retrieve_from", new Object[]
5244                                   { dbname }));
5245                   ifetch.add(fetchr);
5246                   ++i;
5247                   if (++icomp >= mcomp || i == (otherdb.size()))
5248                   {
5249                     ifetch.setText(MessageManager.formatMessage(
5250                             "label.source_to_target", imname, sname));
5251                     dfetch.add(ifetch);
5252                     ifetch = new JMenu();
5253                     imname = null;
5254                     icomp = 0;
5255                     comp++;
5256                   }
5257                 }
5258               }
5259               ++dbi;
5260               if (comp >= mcomp || dbi >= (dbclasses.length))
5261               {
5262                 dfetch.setText(MessageManager.formatMessage(
5263                         "label.source_to_target", mname, dbclass));
5264                 rfetch.add(dfetch);
5265                 dfetch = new JMenu();
5266                 mname = null;
5267                 comp = 0;
5268               }
5269             }
5270           }
5271         });
5272       }
5273     }).start();
5274
5275   }
5276
5277   /**
5278    * Left justify the whole alignment.
5279    */
5280   @Override
5281   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5282   {
5283     AlignmentI al = viewport.getAlignment();
5284     al.justify(false);
5285     viewport.firePropertyChange("alignment", null, al);
5286   }
5287
5288   /**
5289    * Right justify the whole alignment.
5290    */
5291   @Override
5292   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5293   {
5294     AlignmentI al = viewport.getAlignment();
5295     al.justify(true);
5296     viewport.firePropertyChange("alignment", null, al);
5297   }
5298
5299   @Override
5300   public void setShowSeqFeatures(boolean b)
5301   {
5302     showSeqFeatures.setSelected(b);
5303     viewport.setShowSequenceFeatures(b);
5304   }
5305
5306   /*
5307    * (non-Javadoc)
5308    *
5309    * @see
5310    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5311    * awt.event.ActionEvent)
5312    */
5313   @Override
5314   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5315   {
5316     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5317     alignPanel.paintAlignment(false, false);
5318   }
5319
5320   /*
5321    * (non-Javadoc)
5322    *
5323    * @see
5324    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5325    * .ActionEvent)
5326    */
5327   @Override
5328   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5329   {
5330     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5331     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5332
5333   }
5334
5335   /*
5336    * (non-Javadoc)
5337    *
5338    * @see
5339    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5340    * .event.ActionEvent)
5341    */
5342   @Override
5343   protected void showGroupConservation_actionPerformed(ActionEvent e)
5344   {
5345     viewport.setShowGroupConservation(showGroupConservation.getState());
5346     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5347   }
5348
5349   /*
5350    * (non-Javadoc)
5351    *
5352    * @see
5353    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5354    * .event.ActionEvent)
5355    */
5356   @Override
5357   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5358   {
5359     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5360     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5361   }
5362
5363   /*
5364    * (non-Javadoc)
5365    *
5366    * @see
5367    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5368    * .event.ActionEvent)
5369    */
5370   @Override
5371   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5372   {
5373     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5374     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5375   }
5376
5377   @Override
5378   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5379   {
5380     showSequenceLogo.setState(true);
5381     viewport.setShowSequenceLogo(true);
5382     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5383     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5384   }
5385
5386   @Override
5387   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5388   {
5389     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5390   }
5391
5392   /*
5393    * (non-Javadoc)
5394    *
5395    * @see
5396    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5397    * .event.ActionEvent)
5398    */
5399   @Override
5400   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5401   {
5402     if (avc.makeGroupsFromSelection())
5403     {
5404       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5405       alignPanel.updateAnnotation();
5406       alignPanel.paintAlignment(true,
5407               viewport.needToUpdateStructureViews());
5408     }
5409   }
5410
5411   public void clearAlignmentSeqRep()
5412   {
5413     // TODO refactor alignmentseqrep to controller
5414     if (viewport.getAlignment().hasSeqrep())
5415     {
5416       viewport.getAlignment().setSeqrep(null);
5417       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5418       alignPanel.updateAnnotation();
5419       alignPanel.paintAlignment(true, true);
5420     }
5421   }
5422
5423   @Override
5424   protected void createGroup_actionPerformed(ActionEvent e)
5425   {
5426     if (avc.createGroup())
5427     {
5428       if (applyAutoAnnotationSettings.isSelected())
5429       {
5430         alignPanel.updateAnnotation(true, false);
5431       }
5432       alignPanel.alignmentChanged();
5433     }
5434   }
5435
5436   @Override
5437   protected void unGroup_actionPerformed(ActionEvent e)
5438   {
5439     if (avc.unGroup())
5440     {
5441       alignPanel.alignmentChanged();
5442     }
5443   }
5444
5445   /**
5446    * make the given alignmentPanel the currently selected tab
5447    *
5448    * @param alignmentPanel
5449    */
5450   public void setDisplayedView(AlignmentPanel alignmentPanel)
5451   {
5452     if (!viewport.getSequenceSetId()
5453             .equals(alignmentPanel.av.getSequenceSetId()))
5454     {
5455       throw new Error(MessageManager.getString(
5456               "error.implementation_error_cannot_show_view_alignment_frame"));
5457     }
5458     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5459             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5460     {
5461       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5462     }
5463   }
5464
5465   /**
5466    * Action on selection of menu options to Show or Hide annotations.
5467    *
5468    * @param visible
5469    * @param forSequences
5470    *          update sequence-related annotations
5471    * @param forAlignment
5472    *          update non-sequence-related annotations
5473    */
5474   @Override
5475   protected void setAnnotationsVisibility(boolean visible,
5476           boolean forSequences, boolean forAlignment)
5477   {
5478     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5479             .getAlignmentAnnotation();
5480     if (anns == null)
5481     {
5482       return;
5483     }
5484     for (AlignmentAnnotation aa : anns)
5485     {
5486       /*
5487        * don't display non-positional annotations on an alignment
5488        */
5489       if (aa.annotations == null)
5490       {
5491         continue;
5492       }
5493       boolean apply = (aa.sequenceRef == null && forAlignment)
5494               || (aa.sequenceRef != null && forSequences);
5495       if (apply)
5496       {
5497         aa.visible = visible;
5498       }
5499     }
5500     alignPanel.validateAnnotationDimensions(true);
5501     alignPanel.alignmentChanged();
5502   }
5503
5504   /**
5505    * Store selected annotation sort order for the view and repaint.
5506    */
5507   @Override
5508   protected void sortAnnotations_actionPerformed()
5509   {
5510     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5511     this.alignPanel.av
5512             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5513     alignPanel.paintAlignment(false, false);
5514   }
5515
5516   /**
5517    *
5518    * @return alignment panels in this alignment frame
5519    */
5520   public List<? extends AlignmentViewPanel> getAlignPanels()
5521   {
5522     // alignPanels is never null
5523     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5524     return alignPanels;
5525   }
5526
5527   /**
5528    * Open a new alignment window, with the cDNA associated with this (protein)
5529    * alignment, aligned as is the protein.
5530    */
5531   protected void viewAsCdna_actionPerformed()
5532   {
5533     // TODO no longer a menu action - refactor as required
5534     final AlignmentI alignment = getViewport().getAlignment();
5535     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5536     if (mappings == null)
5537     {
5538       return;
5539     }
5540     List<SequenceI> cdnaSeqs = new ArrayList<>();
5541     for (SequenceI aaSeq : alignment.getSequences())
5542     {
5543       for (AlignedCodonFrame acf : mappings)
5544       {
5545         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5546         if (dnaSeq != null)
5547         {
5548           /*
5549            * There is a cDNA mapping for this protein sequence - add to new
5550            * alignment. It will share the same dataset sequence as other mapped
5551            * cDNA (no new mappings need to be created).
5552            */
5553           final Sequence newSeq = new Sequence(dnaSeq);
5554           newSeq.setDatasetSequence(dnaSeq);
5555           cdnaSeqs.add(newSeq);
5556         }
5557       }
5558     }
5559     if (cdnaSeqs.size() == 0)
5560     {
5561       // show a warning dialog no mapped cDNA
5562       return;
5563     }
5564     AlignmentI cdna = new Alignment(
5565             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5566     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5567             AlignFrame.DEFAULT_HEIGHT);
5568     cdna.alignAs(alignment);
5569     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5570             + this.title;
5571     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5572             AlignFrame.DEFAULT_HEIGHT);
5573   }
5574
5575   /**
5576    * Set visibility of dna/protein complement view (available when shown in a
5577    * split frame).
5578    *
5579    * @param show
5580    */
5581   @Override
5582   protected void showComplement_actionPerformed(boolean show)
5583   {
5584     SplitContainerI sf = getSplitViewContainer();
5585     if (sf != null)
5586     {
5587       sf.setComplementVisible(this, show);
5588     }
5589   }
5590
5591   /**
5592    * Generate the reverse (optionally complemented) of the selected sequences,
5593    * and add them to the alignment
5594    */
5595   @Override
5596   protected void showReverse_actionPerformed(boolean complement)
5597   {
5598     AlignmentI al = null;
5599     try
5600     {
5601       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5602       al = dna.reverseCdna(complement);
5603       viewport.addAlignment(al, "");
5604       addHistoryItem(new EditCommand(
5605               MessageManager.getString("label.add_sequences"), Action.PASTE,
5606               al.getSequencesArray(), 0, al.getWidth(),
5607               viewport.getAlignment()));
5608     } catch (Exception ex)
5609     {
5610       System.err.println(ex.getMessage());
5611       return;
5612     }
5613   }
5614
5615   /**
5616    * Try to run a script in the Groovy console, having first ensured that this
5617    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5618    * be targeted at this alignment.
5619    */
5620   @Override
5621   protected void runGroovy_actionPerformed()
5622   {
5623     Jalview.setCurrentAlignFrame(this);
5624     groovy.ui.Console console = Desktop.getGroovyConsole();
5625     if (console != null)
5626     {
5627       try
5628       {
5629         console.runScript();
5630       } catch (Exception ex)
5631       {
5632         System.err.println((ex.toString()));
5633         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5634                 MessageManager.getString("label.couldnt_run_groovy_script"),
5635                 MessageManager.getString("label.groovy_support_failed"),
5636                 JvOptionPane.ERROR_MESSAGE);
5637       }
5638     }
5639     else
5640     {
5641       System.err.println("Can't run Groovy script as console not found");
5642     }
5643   }
5644
5645   /**
5646    * Hides columns containing (or not containing) a specified feature, provided
5647    * that would not leave all columns hidden
5648    *
5649    * @param featureType
5650    * @param columnsContaining
5651    * @return
5652    */
5653   public boolean hideFeatureColumns(String featureType,
5654           boolean columnsContaining)
5655   {
5656     boolean notForHiding = avc.markColumnsContainingFeatures(
5657             columnsContaining, false, false, featureType);
5658     if (notForHiding)
5659     {
5660       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5661               false, featureType))
5662       {
5663         getViewport().hideSelectedColumns();
5664         return true;
5665       }
5666     }
5667     return false;
5668   }
5669
5670   @Override
5671   protected void selectHighlightedColumns_actionPerformed(
5672           ActionEvent actionEvent)
5673   {
5674     // include key modifier check in case user selects from menu
5675     avc.markHighlightedColumns(
5676             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5677             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5678                     | ActionEvent.CTRL_MASK)) != 0);
5679   }
5680
5681   /**
5682    * Rebuilds the Colour menu, including any user-defined colours which have
5683    * been loaded either on startup or during the session
5684    */
5685   public void buildColourMenu()
5686   {
5687     colourMenu.removeAll();
5688
5689     colourMenu.add(applyToAllGroups);
5690     colourMenu.add(textColour);
5691     colourMenu.addSeparator();
5692
5693     ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5694             viewport.getAlignment(), false);
5695
5696     colourMenu.add(annotationColour);
5697     bg.add(annotationColour);
5698     colourMenu.addSeparator();
5699     colourMenu.add(conservationMenuItem);
5700     colourMenu.add(modifyConservation);
5701     colourMenu.add(abovePIDThreshold);
5702     colourMenu.add(modifyPID);
5703
5704     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5705     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5706   }
5707
5708   /**
5709    * Open a dialog (if not already open) that allows the user to select and
5710    * calculate PCA or Tree analysis
5711    */
5712   protected void openTreePcaDialog()
5713   {
5714     if (alignPanel.getCalculationDialog() == null)
5715     {
5716       new CalculationChooser(AlignFrame.this);
5717     }
5718   }
5719
5720   @Override
5721   protected void loadVcf_actionPerformed()
5722   {
5723     JalviewFileChooser chooser = new JalviewFileChooser(
5724             Cache.getProperty("LAST_DIRECTORY"));
5725     chooser.setFileView(new JalviewFileView());
5726     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5727     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5728     final AlignFrame us = this;
5729     chooser.setResponseHandler(0, new Runnable()
5730     {
5731       @Override
5732       public void run()
5733       {
5734         String choice = chooser.getSelectedFile().getPath();
5735         Cache.setProperty("LAST_DIRECTORY", choice);
5736         SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5737         new VCFLoader(choice).loadVCF(seqs, us);
5738       }
5739     });
5740     chooser.showOpenDialog(null);
5741
5742   }
5743
5744 }
5745
5746 class PrintThread extends Thread
5747 {
5748   AlignmentPanel ap;
5749
5750   public PrintThread(AlignmentPanel ap)
5751   {
5752     this.ap = ap;
5753   }
5754
5755   static PageFormat pf;
5756
5757   @Override
5758   public void run()
5759   {
5760     PrinterJob printJob = PrinterJob.getPrinterJob();
5761
5762     if (pf != null)
5763     {
5764       printJob.setPrintable(ap, pf);
5765     }
5766     else
5767     {
5768       printJob.setPrintable(ap);
5769     }
5770
5771     if (printJob.printDialog())
5772     {
5773       try
5774       {
5775         printJob.print();
5776       } catch (Exception PrintException)
5777       {
5778         PrintException.printStackTrace();
5779       }
5780     }
5781   }
5782 }