src/jalview/gui/AlignFrame.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.analysis.AlignmentSorter;
  24 import jalview.analysis.AlignmentUtils;
  25 import jalview.analysis.CrossRef;
  26 import jalview.analysis.Dna;
  27 import jalview.analysis.ParseProperties;
  28 import jalview.analysis.SequenceIdMatcher;
  29 import jalview.api.AlignExportSettingsI;
  30 import jalview.api.AlignViewControllerGuiI;
  31 import jalview.api.AlignViewControllerI;
  32 import jalview.api.AlignViewportI;
  33 import jalview.api.AlignmentViewPanel;
  34 import jalview.api.FeatureSettingsControllerI;
  35 import jalview.api.SplitContainerI;
  36 import jalview.api.ViewStyleI;
  37 import jalview.api.analysis.SimilarityParamsI;
  38 import jalview.bin.Cache;
  39 import jalview.bin.Jalview;
  40 import jalview.commands.CommandI;
  41 import jalview.commands.EditCommand;
  42 import jalview.commands.EditCommand.Action;
  43 import jalview.commands.OrderCommand;
  44 import jalview.commands.RemoveGapColCommand;
  45 import jalview.commands.RemoveGapsCommand;
  46 import jalview.commands.SlideSequencesCommand;
  47 import jalview.commands.TrimRegionCommand;
  48 import jalview.datamodel.AlignExportSettingsAdapter;
  49 import jalview.datamodel.AlignedCodonFrame;
  50 import jalview.datamodel.Alignment;
  51 import jalview.datamodel.AlignmentAnnotation;
  52 import jalview.datamodel.AlignmentExportData;
  53 import jalview.datamodel.AlignmentI;
  54 import jalview.datamodel.AlignmentOrder;
  55 import jalview.datamodel.AlignmentView;
  56 import jalview.datamodel.ColumnSelection;
  57 import jalview.datamodel.HiddenColumns;
  58 import jalview.datamodel.PDBEntry;
  59 import jalview.datamodel.SeqCigar;
  60 import jalview.datamodel.Sequence;
  61 import jalview.datamodel.SequenceGroup;
  62 import jalview.datamodel.SequenceI;
  63 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  64 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
  65 import jalview.io.AlignmentProperties;
  66 import jalview.io.AnnotationFile;
  67 import jalview.io.BioJsHTMLOutput;
  68 import jalview.io.DataSourceType;
  69 import jalview.io.FileFormat;
  70 import jalview.io.FileFormatI;
  71 import jalview.io.FileFormats;
  72 import jalview.io.FileLoader;
  73 import jalview.io.FileParse;
  74 import jalview.io.FormatAdapter;
  75 import jalview.io.HtmlSvgOutput;
  76 import jalview.io.IdentifyFile;
  77 import jalview.io.JPredFile;
  78 import jalview.io.JalviewFileChooser;
  79 import jalview.io.JalviewFileView;
  80 import jalview.io.JnetAnnotationMaker;
  81 import jalview.io.NewickFile;
  82 import jalview.io.ScoreMatrixFile;
  83 import jalview.io.TCoffeeScoreFile;
  84 import jalview.io.vcf.VCFLoader;
  85 import jalview.jbgui.GAlignFrame;
  86 import jalview.schemes.ColourSchemeI;
  87 import jalview.schemes.ColourSchemes;
  88 import jalview.schemes.ResidueColourScheme;
  89 import jalview.schemes.TCoffeeColourScheme;
  90 import jalview.util.ImageMaker.TYPE;
  91 import jalview.util.MessageManager;
  92 import jalview.util.Platform;
  93 import jalview.viewmodel.AlignmentViewport;
  94 import jalview.viewmodel.ViewportRanges;
  95 import jalview.ws.DBRefFetcher;
  96 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
  97 import jalview.ws.jws1.Discoverer;
  98 import jalview.ws.jws2.Jws2Discoverer;
  99 import jalview.ws.jws2.jabaws2.Jws2Instance;
 100 import jalview.ws.seqfetcher.DbSourceProxy;
 101
 102 import java.awt.BorderLayout;
 103 import java.awt.Color;
 104 import java.awt.Component;
 105 import java.awt.Rectangle;
 106 import java.awt.Toolkit;
 107 import java.awt.datatransfer.Clipboard;
 108 import java.awt.datatransfer.DataFlavor;
 109 import java.awt.datatransfer.StringSelection;
 110 import java.awt.datatransfer.Transferable;
 111 import java.awt.dnd.DnDConstants;
 112 import java.awt.dnd.DropTargetDragEvent;
 113 import java.awt.dnd.DropTargetDropEvent;
 114 import java.awt.dnd.DropTargetEvent;
 115 import java.awt.dnd.DropTargetListener;
 116 import java.awt.event.ActionEvent;
 117 import java.awt.event.ActionListener;
 118 import java.awt.event.FocusAdapter;
 119 import java.awt.event.FocusEvent;
 120 import java.awt.event.ItemEvent;
 121 import java.awt.event.ItemListener;
 122 import java.awt.event.KeyAdapter;
 123 import java.awt.event.KeyEvent;
 124 import java.awt.event.MouseEvent;
 125 import java.awt.print.PageFormat;
 126 import java.awt.print.PrinterJob;
 127 import java.beans.PropertyChangeEvent;
 128 import java.io.File;
 129 import java.io.FileWriter;
 130 import java.io.PrintWriter;
 131 import java.net.URL;
 132 import java.util.ArrayList;
 133 import java.util.Arrays;
 134 import java.util.Deque;
 135 import java.util.Enumeration;
 136 import java.util.Hashtable;
 137 import java.util.List;
 138 import java.util.Vector;
 139
 140 import javax.swing.JCheckBoxMenuItem;
 141 import javax.swing.JComponent;
 142 import javax.swing.JEditorPane;
 143 import javax.swing.JInternalFrame;
 144 import javax.swing.JLabel;
 145 import javax.swing.JLayeredPane;
 146 import javax.swing.JMenu;
 147 import javax.swing.JMenuItem;
 148 import javax.swing.JPanel;
 149 import javax.swing.JScrollPane;
 150 import javax.swing.SwingUtilities;
 151
 152 /**
 153  * DOCUMENT ME!
 154  *
 155  * @author $author$
 156  * @version $Revision$
 157  */
 158 public class AlignFrame extends GAlignFrame implements DropTargetListener,
 159         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 160 {
 161
 162   public static final int DEFAULT_WIDTH = 700;
 163
 164   public static final int DEFAULT_HEIGHT = 500;
 165
 166   /*
 167    * The currently displayed panel (selected tabbed view if more than one)
 168    */
 169   public AlignmentPanel alignPanel;
 170
 171   AlignViewport viewport;
 172
 173   public AlignViewControllerI avc;
 174
 175   List<AlignmentPanel> alignPanels = new ArrayList<>();
 176
 177   /**
 178    * Last format used to load or save alignments in this window
 179    */
 180   FileFormatI currentFileFormat = null;
 181
 182   /**
 183    * Current filename for this alignment
 184    */
 185   String fileName = null;
 186
 187   File fileObject;
 188
 189   /**
 190    * Creates a new AlignFrame object with specific width and height.
 191    *
 192    * @param al
 193    * @param width
 194    * @param height
 195    */
 196   public AlignFrame(AlignmentI al, int width, int height)
 197   {
 198     this(al, null, width, height);
 199   }
 200
 201   /**
 202    * Creates a new AlignFrame object with specific width, height and
 203    * sequenceSetId
 204    *
 205    * @param al
 206    * @param width
 207    * @param height
 208    * @param sequenceSetId
 209    */
 210   public AlignFrame(AlignmentI al, int width, int height,
 211           String sequenceSetId)
 212   {
 213     this(al, null, width, height, sequenceSetId);
 214   }
 215
 216   /**
 217    * Creates a new AlignFrame object with specific width, height and
 218    * sequenceSetId
 219    *
 220    * @param al
 221    * @param width
 222    * @param height
 223    * @param sequenceSetId
 224    * @param viewId
 225    */
 226   public AlignFrame(AlignmentI al, int width, int height,
 227           String sequenceSetId, String viewId)
 228   {
 229     this(al, null, width, height, sequenceSetId, viewId);
 230   }
 231
 232   /**
 233    * new alignment window with hidden columns
 234    *
 235    * @param al
 236    *          AlignmentI
 237    * @param hiddenColumns
 238    *          ColumnSelection or null
 239    * @param width
 240    *          Width of alignment frame
 241    * @param height
 242    *          height of frame.
 243    */
 244   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 245           int height)
 246   {
 247     this(al, hiddenColumns, width, height, null);
 248   }
 249
 250   /**
 251    * Create alignment frame for al with hiddenColumns, a specific width and
 252    * height, and specific sequenceId
 253    *
 254    * @param al
 255    * @param hiddenColumns
 256    * @param width
 257    * @param height
 258    * @param sequenceSetId
 259    *          (may be null)
 260    */
 261   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 262           int height, String sequenceSetId)
 263   {
 264     this(al, hiddenColumns, width, height, sequenceSetId, null);
 265   }
 266
 267   /**
 268    * Create alignment frame for al with hiddenColumns, a specific width and
 269    * height, and specific sequenceId
 270    *
 271    * @param al
 272    * @param hiddenColumns
 273    * @param width
 274    * @param height
 275    * @param sequenceSetId
 276    *          (may be null)
 277    * @param viewId
 278    *          (may be null)
 279    */
 280   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
 281           int height, String sequenceSetId, String viewId)
 282   {
 283     setSize(width, height);
 284
 285     if (al.getDataset() == null)
 286     {
 287       al.setDataset(null);
 288     }
 289
 290     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 291
 292     alignPanel = new AlignmentPanel(this, viewport);
 293
 294     addAlignmentPanel(alignPanel, true);
 295     init();
 296   }
 297
 298   public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
 299           HiddenColumns hiddenColumns, int width, int height)
 300   {
 301     setSize(width, height);
 302
 303     if (al.getDataset() == null)
 304     {
 305       al.setDataset(null);
 306     }
 307
 308     viewport = new AlignViewport(al, hiddenColumns);
 309
 310     if (hiddenSeqs != null && hiddenSeqs.length > 0)
 311     {
 312       viewport.hideSequence(hiddenSeqs);
 313     }
 314     alignPanel = new AlignmentPanel(this, viewport);
 315     addAlignmentPanel(alignPanel, true);
 316     init();
 317   }
 318
 319   /**
 320    * Make a new AlignFrame from existing alignmentPanels
 321    *
 322    * @param ap
 323    *          AlignmentPanel
 324    * @param av
 325    *          AlignViewport
 326    */
 327   public AlignFrame(AlignmentPanel ap)
 328   {
 329     viewport = ap.av;
 330     alignPanel = ap;
 331     addAlignmentPanel(ap, false);
 332     init();
 333   }
 334
 335   /**
 336    * initalise the alignframe from the underlying viewport data and the
 337    * configurations
 338    */
 339   void init()
 340   {
 341 //        setBackground(Color.white); // BH 2019
 342
 343     if (!Jalview.isHeadlessMode())
 344     {
 345       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
 346     }
 347
 348     avc = new jalview.controller.AlignViewController(this, viewport,
 349             alignPanel);
 350     if (viewport.getAlignmentConservationAnnotation() == null)
 351     {
 352       // BLOSUM62Colour.setEnabled(false);
 353       conservationMenuItem.setEnabled(false);
 354       modifyConservation.setEnabled(false);
 355       // PIDColour.setEnabled(false);
 356       // abovePIDThreshold.setEnabled(false);
 357       // modifyPID.setEnabled(false);
 358     }
 359
 360     String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
 361             "No sort");
 362
 363     if (sortby.equals("Id"))
 364     {
 365       sortIDMenuItem_actionPerformed(null);
 366     }
 367     else if (sortby.equals("Pairwise Identity"))
 368     {
 369       sortPairwiseMenuItem_actionPerformed(null);
 370     }
 371
 372     this.alignPanel.av
 373             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 374
 375     setMenusFromViewport(viewport);
 376     buildSortByAnnotationScoresMenu();
 377     calculateTree.addActionListener(new ActionListener()
 378     {
 379
 380       @Override
 381       public void actionPerformed(ActionEvent e)
 382       {
 383         openTreePcaDialog();
 384       }
 385     });
 386     buildColourMenu();
 387
 388     if (Desktop.desktop != null)
 389     {
 390       this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
 391       /**
 392        * BH 2018 ignore service listeners
 393        *
 394        * @j2sNative
 395        *
 396        */
 397       {
 398         addServiceListeners();
 399       }
 400       setGUINucleotide();
 401     }
 402
 403     if (viewport.getWrapAlignment())
 404     {
 405       wrapMenuItem_actionPerformed(null);
 406     }
 407
 408     if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
 409     {
 410       this.overviewMenuItem_actionPerformed(null);
 411     }
 412
 413     addKeyListener();
 414
 415     final List<AlignmentPanel> selviews = new ArrayList<>();
 416     final List<AlignmentPanel> origview = new ArrayList<>();
 417     final String menuLabel = MessageManager
 418             .getString("label.copy_format_from");
 419     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
 420             new ViewSetProvider()
 421             {
 422
 423               @Override
 424               public AlignmentPanel[] getAllAlignmentPanels()
 425               {
 426                 origview.clear();
 427                 origview.add(alignPanel);
 428                 // make an array of all alignment panels except for this one
 429                 List<AlignmentPanel> aps = new ArrayList<>(
 430                         Arrays.asList(Desktop.getAlignmentPanels(null)));
 431                 aps.remove(AlignFrame.this.alignPanel);
 432                 return aps.toArray(new AlignmentPanel[aps.size()]);
 433               }
 434             }, selviews, new ItemListener()
 435             {
 436
 437               @Override
 438               public void itemStateChanged(ItemEvent e)
 439               {
 440                 if (origview.size() > 0)
 441                 {
 442                   final AlignmentPanel ap = origview.get(0);
 443
 444                   /*
 445                    * Copy the ViewStyle of the selected panel to 'this one'.
 446                    * Don't change value of 'scaleProteinAsCdna' unless copying
 447                    * from a SplitFrame.
 448                    */
 449                   ViewStyleI vs = selviews.get(0).getAlignViewport()
 450                           .getViewStyle();
 451                   boolean fromSplitFrame = selviews.get(0)
 452                           .getAlignViewport().getCodingComplement() != null;
 453                   if (!fromSplitFrame)
 454                   {
 455                     vs.setScaleProteinAsCdna(ap.getAlignViewport()
 456                             .getViewStyle().isScaleProteinAsCdna());
 457                   }
 458                   ap.getAlignViewport().setViewStyle(vs);
 459
 460                   /*
 461                    * Also rescale ViewStyle of SplitFrame complement if there is
 462                    * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
 463                    * the whole ViewStyle (allow cDNA protein to have different
 464                    * fonts)
 465                    */
 466                   AlignViewportI complement = ap.getAlignViewport()
 467                           .getCodingComplement();
 468                   if (complement != null && vs.isScaleProteinAsCdna())
 469                   {
 470                     AlignFrame af = Desktop.getAlignFrameFor(complement);
 471                     ((SplitFrame) af.getSplitViewContainer())
 472                             .adjustLayout();
 473                     af.setMenusForViewport();
 474                   }
 475
 476                   ap.updateLayout();
 477                   ap.setSelected(true);
 478                   ap.alignFrame.setMenusForViewport();
 479
 480                 }
 481               }
 482             });
 483     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 484             .indexOf("devel") > -1
 485             || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
 486                     .indexOf("test") > -1)
 487     {
 488       formatMenu.add(vsel);
 489     }
 490     addFocusListener(new FocusAdapter()
 491     {
 492       @Override
 493       public void focusGained(FocusEvent e)
 494       {
 495         Jalview.setCurrentAlignFrame(AlignFrame.this);
 496       }
 497     });
 498
 499   }
 500
 501   /**
 502    * Change the filename and format for the alignment, and enable the 'reload'
 503    * button functionality.
 504    *
 505    * @param file
 506    *          valid filename
 507    * @param format
 508    *          format of file
 509    */
 510   public void setFileName(String file, FileFormatI format)
 511   {
 512     fileName = file;
 513     setFileFormat(format);
 514     reload.setEnabled(true);
 515   }
 516
 517   /**
 518    * JavaScript will have this, maybe others. More dependable than a file name
 519    * and maintains a reference to the actual bytes loaded.
 520    *
 521    * @param file
 522    */
 523   public void setFileObject(File file)
 524   {
 525     this.fileObject = file;
 526   }
 527
 528   /**
 529    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
 530    * events
 531    */
 532   void addKeyListener()
 533   {
 534     addKeyListener(new KeyAdapter()
 535     {
 536       @Override
 537       public void keyPressed(KeyEvent evt)
 538       {
 539         if (viewport.cursorMode
 540                 && ((evt.getKeyCode() >= KeyEvent.VK_0
 541                         && evt.getKeyCode() <= KeyEvent.VK_9)
 542                         || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
 543                                 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
 544                 && Character.isDigit(evt.getKeyChar()))
 545         {
 546           alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
 547         }
 548
 549         switch (evt.getKeyCode())
 550         {
 551
 552         case 27: // escape key
 553           deselectAllSequenceMenuItem_actionPerformed(null);
 554
 555           break;
 556
 557         case KeyEvent.VK_DOWN:
 558           if (evt.isAltDown() || !viewport.cursorMode)
 559           {
 560             moveSelectedSequences(false);
 561           }
 562           if (viewport.cursorMode)
 563           {
 564             alignPanel.getSeqPanel().moveCursor(0, 1);
 565           }
 566           break;
 567
 568         case KeyEvent.VK_UP:
 569           if (evt.isAltDown() || !viewport.cursorMode)
 570           {
 571             moveSelectedSequences(true);
 572           }
 573           if (viewport.cursorMode)
 574           {
 575             alignPanel.getSeqPanel().moveCursor(0, -1);
 576           }
 577
 578           break;
 579
 580         case KeyEvent.VK_LEFT:
 581           if (evt.isAltDown() || !viewport.cursorMode)
 582           {
 583             slideSequences(false,
 584                     alignPanel.getSeqPanel().getKeyboardNo1());
 585           }
 586           else
 587           {
 588             alignPanel.getSeqPanel().moveCursor(-1, 0);
 589           }
 590
 591           break;
 592
 593         case KeyEvent.VK_RIGHT:
 594           if (evt.isAltDown() || !viewport.cursorMode)
 595           {
 596             slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
 597           }
 598           else
 599           {
 600             alignPanel.getSeqPanel().moveCursor(1, 0);
 601           }
 602           break;
 603
 604         case KeyEvent.VK_SPACE:
 605           if (viewport.cursorMode)
 606           {
 607             alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
 608                     || evt.isShiftDown() || evt.isAltDown());
 609           }
 610           break;
 611
 612         // case KeyEvent.VK_A:
 613         // if (viewport.cursorMode)
 614         // {
 615         // alignPanel.seqPanel.insertNucAtCursor(false,"A");
 616         // //System.out.println("A");
 617         // }
 618         // break;
 619         /*
 620          * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
 621          * System.out.println("closing bracket"); } break;
 622          */
 623         case KeyEvent.VK_DELETE:
 624         case KeyEvent.VK_BACK_SPACE:
 625           if (!viewport.cursorMode)
 626           {
 627             cut_actionPerformed(null);
 628           }
 629           else
 630           {
 631             alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
 632                     || evt.isShiftDown() || evt.isAltDown());
 633           }
 634
 635           break;
 636
 637         case KeyEvent.VK_S:
 638           if (viewport.cursorMode)
 639           {
 640             alignPanel.getSeqPanel().setCursorRow();
 641           }
 642           break;
 643         case KeyEvent.VK_C:
 644           if (viewport.cursorMode && !evt.isControlDown())
 645           {
 646             alignPanel.getSeqPanel().setCursorColumn();
 647           }
 648           break;
 649         case KeyEvent.VK_P:
 650           if (viewport.cursorMode)
 651           {
 652             alignPanel.getSeqPanel().setCursorPosition();
 653           }
 654           break;
 655
 656         case KeyEvent.VK_ENTER:
 657         case KeyEvent.VK_COMMA:
 658           if (viewport.cursorMode)
 659           {
 660             alignPanel.getSeqPanel().setCursorRowAndColumn();
 661           }
 662           break;
 663
 664         case KeyEvent.VK_Q:
 665           if (viewport.cursorMode)
 666           {
 667             alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
 668           }
 669           break;
 670         case KeyEvent.VK_M:
 671           if (viewport.cursorMode)
 672           {
 673             alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
 674           }
 675           break;
 676
 677         case KeyEvent.VK_F2:
 678           viewport.cursorMode = !viewport.cursorMode;
 679           setStatus(MessageManager
 680                   .formatMessage("label.keyboard_editing_mode", new String[]
 681                   { (viewport.cursorMode ? "on" : "off") }));
 682           if (viewport.cursorMode)
 683           {
 684             ViewportRanges ranges = viewport.getRanges();
 685             alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
 686                     .getStartRes();
 687             alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
 688                     .getStartSeq();
 689           }
 690           alignPanel.getSeqPanel().seqCanvas.repaint();
 691           break;
 692
 693         case KeyEvent.VK_F1:
 694           try
 695           {
 696             Help.showHelpWindow();
 697           } catch (Exception ex)
 698           {
 699             ex.printStackTrace();
 700           }
 701           break;
 702         case KeyEvent.VK_H:
 703         {
 704           boolean toggleSeqs = !evt.isControlDown();
 705           boolean toggleCols = !evt.isShiftDown();
 706           toggleHiddenRegions(toggleSeqs, toggleCols);
 707           break;
 708         }
 709         case KeyEvent.VK_B:
 710         {
 711           boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
 712           boolean modifyExisting = true; // always modify, don't clear
 713                                          // evt.isShiftDown();
 714           boolean invertHighlighted = evt.isAltDown();
 715           avc.markHighlightedColumns(invertHighlighted, modifyExisting,
 716                   toggleSel);
 717           break;
 718         }
 719         case KeyEvent.VK_PAGE_UP:
 720           viewport.getRanges().pageUp();
 721           break;
 722         case KeyEvent.VK_PAGE_DOWN:
 723           viewport.getRanges().pageDown();
 724           break;
 725         }
 726       }
 727
 728       @Override
 729       public void keyReleased(KeyEvent evt)
 730       {
 731         switch (evt.getKeyCode())
 732         {
 733         case KeyEvent.VK_LEFT:
 734           if (evt.isAltDown() || !viewport.cursorMode)
 735           {
 736             viewport.firePropertyChange("alignment", null,
 737                     viewport.getAlignment().getSequences());
 738           }
 739           break;
 740
 741         case KeyEvent.VK_RIGHT:
 742           if (evt.isAltDown() || !viewport.cursorMode)
 743           {
 744             viewport.firePropertyChange("alignment", null,
 745                     viewport.getAlignment().getSequences());
 746           }
 747           break;
 748         }
 749       }
 750     });
 751   }
 752
 753   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
 754   {
 755     ap.alignFrame = this;
 756     avc = new jalview.controller.AlignViewController(this, viewport,
 757             alignPanel);
 758
 759     alignPanels.add(ap);
 760
 761     PaintRefresher.Register(ap, ap.av.getSequenceSetId());
 762
 763     int aSize = alignPanels.size();
 764
 765     tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 766
 767     if (aSize == 1 && ap.av.getViewName() == null)
 768     {
 769       this.getContentPane().add(ap, BorderLayout.CENTER);
 770     }
 771     else
 772     {
 773       if (aSize == 2)
 774       {
 775         setInitialTabVisible();
 776       }
 777
 778       expandViews.setEnabled(true);
 779       gatherViews.setEnabled(true);
 780       tabbedPane.addTab(ap.av.getViewName(), ap);
 781
 782       ap.setVisible(false);
 783     }
 784
 785     if (newPanel)
 786     {
 787       if (ap.av.isPadGaps())
 788       {
 789         ap.av.getAlignment().padGaps();
 790       }
 791       ap.av.updateConservation(ap);
 792       ap.av.updateConsensus(ap);
 793       ap.av.updateStrucConsensus(ap);
 794     }
 795   }
 796
 797   public void setInitialTabVisible()
 798   {
 799     expandViews.setEnabled(true);
 800     gatherViews.setEnabled(true);
 801     tabbedPane.setVisible(true);
 802     AlignmentPanel first = alignPanels.get(0);
 803     tabbedPane.addTab(first.av.getViewName(), first);
 804     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
 805   }
 806
 807   public AlignViewport getViewport()
 808   {
 809     return viewport;
 810   }
 811
 812   /* Set up intrinsic listeners for dynamically generated GUI bits. */
 813   private void addServiceListeners()
 814   {
 815     final java.beans.PropertyChangeListener thisListener;
 816     Desktop.instance.addJalviewPropertyChangeListener("services",
 817             thisListener = new java.beans.PropertyChangeListener()
 818             {
 819               @Override
 820               public void propertyChange(PropertyChangeEvent evt)
 821               {
 822                 // // System.out.println("Discoverer property change.");
 823                 // if (evt.getPropertyName().equals("services"))
 824                 {
 825                   SwingUtilities.invokeLater(new Runnable()
 826                   {
 827
 828                     @Override
 829                     public void run()
 830                     {
 831                       System.err.println(
 832                               "Rebuild WS Menu for service change");
 833                       BuildWebServiceMenu();
 834                     }
 835
 836                   });
 837                 }
 838               }
 839             });
 840     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 841     {
 842       @Override
 843       public void internalFrameClosed(
 844               javax.swing.event.InternalFrameEvent evt)
 845       {
 846         // System.out.println("deregistering discoverer listener");
 847         Desktop.instance.removeJalviewPropertyChangeListener("services",
 848                 thisListener);
 849         closeMenuItem_actionPerformed(true);
 850       };
 851     });
 852     // Finally, build the menu once to get current service state
 853     new Thread(new Runnable()
 854     {
 855       @Override
 856       public void run()
 857       {
 858         BuildWebServiceMenu();
 859       }
 860     }).start();
 861   }
 862
 863   /**
 864    * Configure menu items that vary according to whether the alignment is
 865    * nucleotide or protein
 866    */
 867   public void setGUINucleotide()
 868   {
 869     AlignmentI al = getViewport().getAlignment();
 870     boolean nucleotide = al.isNucleotide();
 871
 872     loadVcf.setVisible(nucleotide);
 873     showTranslation.setVisible(nucleotide);
 874     showReverse.setVisible(nucleotide);
 875     showReverseComplement.setVisible(nucleotide);
 876     conservationMenuItem.setEnabled(!nucleotide);
 877     modifyConservation
 878             .setEnabled(!nucleotide && conservationMenuItem.isSelected());
 879     showGroupConservation.setEnabled(!nucleotide);
 880
 881     showComplementMenuItem
 882             .setText(nucleotide ? MessageManager.getString("label.protein")
 883                     : MessageManager.getString("label.nucleotide"));
 884   }
 885
 886   /**
 887    * set up menus for the current viewport. This may be called after any
 888    * operation that affects the data in the current view (selection changed,
 889    * etc) to update the menus to reflect the new state.
 890    */
 891   @Override
 892   public void setMenusForViewport()
 893   {
 894     setMenusFromViewport(viewport);
 895   }
 896
 897   /**
 898    * Need to call this method when tabs are selected for multiple views, or when
 899    * loading from Jalview2XML.java
 900    *
 901    * @param av
 902    *          AlignViewport
 903    */
 904   public void setMenusFromViewport(AlignViewport av)
 905   {
 906     padGapsMenuitem.setSelected(av.isPadGaps());
 907     colourTextMenuItem.setSelected(av.isShowColourText());
 908     abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
 909     modifyPID.setEnabled(abovePIDThreshold.isSelected());
 910     conservationMenuItem.setSelected(av.getConservationSelected());
 911     modifyConservation.setEnabled(conservationMenuItem.isSelected());
 912     seqLimits.setSelected(av.getShowJVSuffix());
 913     idRightAlign.setSelected(av.isRightAlignIds());
 914     centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
 915     renderGapsMenuItem.setSelected(av.isRenderGaps());
 916     wrapMenuItem.setSelected(av.getWrapAlignment());
 917     scaleAbove.setVisible(av.getWrapAlignment());
 918     scaleLeft.setVisible(av.getWrapAlignment());
 919     scaleRight.setVisible(av.getWrapAlignment());
 920     annotationPanelMenuItem.setState(av.isShowAnnotation());
 921     /*
 922      * Show/hide annotations only enabled if annotation panel is shown
 923      */
 924     showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 925     hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
 926     showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 927     hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
 928     viewBoxesMenuItem.setSelected(av.getShowBoxes());
 929     viewTextMenuItem.setSelected(av.getShowText());
 930     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
 931     showGroupConsensus.setSelected(av.isShowGroupConsensus());
 932     showGroupConservation.setSelected(av.isShowGroupConservation());
 933     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
 934     showSequenceLogo.setSelected(av.isShowSequenceLogo());
 935     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
 936
 937     ColourMenuHelper.setColourSelected(colourMenu,
 938             av.getGlobalColourScheme());
 939
 940     showSeqFeatures.setSelected(av.isShowSequenceFeatures());
 941     hiddenMarkers.setState(av.getShowHiddenMarkers());
 942     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
 943     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
 944     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
 945     autoCalculate.setSelected(av.autoCalculateConsensus);
 946     sortByTree.setSelected(av.sortByTree);
 947     listenToViewSelections.setSelected(av.followSelection);
 948
 949     showProducts.setEnabled(canShowProducts());
 950     setGroovyEnabled(Desktop.getGroovyConsole() != null);
 951
 952     updateEditMenuBar();
 953   }
 954
 955   /**
 956    * Set the enabled state of the 'Run Groovy' option in the Calculate menu
 957    *
 958    * @param b
 959    */
 960   public void setGroovyEnabled(boolean b)
 961   {
 962     runGroovy.setEnabled(b);
 963   }
 964
 965   private IProgressIndicator progressBar;
 966
 967   /*
 968    * (non-Javadoc)
 969    *
 970    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
 971    */
 972   @Override
 973   public void setProgressBar(String message, long id)
 974   {
 975     progressBar.setProgressBar(message, id);
 976   }
 977
 978   @Override
 979   public void registerHandler(final long id,
 980           final IProgressIndicatorHandler handler)
 981   {
 982     progressBar.registerHandler(id, handler);
 983   }
 984
 985   /**
 986    *
 987    * @return true if any progress bars are still active
 988    */
 989   @Override
 990   public boolean operationInProgress()
 991   {
 992     return progressBar.operationInProgress();
 993   }
 994
 995   @Override
 996   public void setStatus(String text)
 997   {
 998           // BH note: If text width and height are 0, then the layout manager
 999           // will dispense of it and change the frame height.
1000           // In JavaScript, we use \u00A0  -- unicode "non-breaking space"
1001           // which is the unicode encoding of &nbsp;
1002
1003     statusBar.setText(text == null || text.isEmpty() ? " " : text);
1004   }
1005
1006   /*
1007    * Added so Castor Mapping file can obtain Jalview Version
1008    */
1009   public String getVersion()
1010   {
1011     return jalview.bin.Cache.getProperty("VERSION");
1012   }
1013
1014   public FeatureRenderer getFeatureRenderer()
1015   {
1016     return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1017   }
1018
1019   @Override
1020   public void fetchSequence_actionPerformed()
1021   {
1022     new SequenceFetcher(this);
1023   }
1024
1025   @Override
1026   public void addFromFile_actionPerformed(ActionEvent e)
1027   {
1028     Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1029   }
1030
1031   @Override
1032   public void reload_actionPerformed(ActionEvent e)
1033   {
1034     if (fileName != null)
1035     {
1036       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1037       // originating file's format
1038       // TODO: work out how to recover feature settings for correct view(s) when
1039       // file is reloaded.
1040       if (FileFormat.Jalview.equals(currentFileFormat))
1041       {
1042         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1043         for (int i = 0; i < frames.length; i++)
1044         {
1045           if (frames[i] instanceof AlignFrame && frames[i] != this
1046                   && ((AlignFrame) frames[i]).fileName != null
1047                   && ((AlignFrame) frames[i]).fileName.equals(fileName))
1048           {
1049             try
1050             {
1051               frames[i].setSelected(true);
1052               Desktop.instance.closeAssociatedWindows();
1053             } catch (java.beans.PropertyVetoException ex)
1054             {
1055             }
1056           }
1057
1058         }
1059         Desktop.instance.closeAssociatedWindows();
1060
1061         FileLoader loader = new FileLoader();
1062         DataSourceType protocol = fileName.startsWith("http:")
1063                 ? DataSourceType.URL
1064                 : DataSourceType.FILE;
1065         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1066       }
1067       else
1068       {
1069         Rectangle bounds = this.getBounds();
1070
1071         FileLoader loader = new FileLoader();
1072
1073         AlignFrame newframe = null;
1074
1075         if (fileObject == null)
1076         {
1077
1078           DataSourceType protocol = (fileName.startsWith("http:")
1079                   ? DataSourceType.URL
1080                   : DataSourceType.FILE);
1081           newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1082                   currentFileFormat);
1083         }
1084         else
1085         {
1086           newframe = loader.LoadFileWaitTillLoaded(fileObject,
1087                   DataSourceType.FILE, currentFileFormat);
1088         }
1089
1090         newframe.setBounds(bounds);
1091         if (featureSettings != null && featureSettings.isShowing())
1092         {
1093           final Rectangle fspos = featureSettings.frame.getBounds();
1094           // TODO: need a 'show feature settings' function that takes bounds -
1095           // need to refactor Desktop.addFrame
1096           newframe.featureSettings_actionPerformed(null);
1097           final FeatureSettings nfs = newframe.featureSettings;
1098           SwingUtilities.invokeLater(new Runnable()
1099           {
1100             @Override
1101             public void run()
1102             {
1103               nfs.frame.setBounds(fspos);
1104             }
1105           });
1106           this.featureSettings.close();
1107           this.featureSettings = null;
1108         }
1109         this.closeMenuItem_actionPerformed(true);
1110       }
1111     }
1112   }
1113
1114   @Override
1115   public void addFromText_actionPerformed(ActionEvent e)
1116   {
1117     Desktop.instance
1118             .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1119   }
1120
1121   @Override
1122   public void addFromURL_actionPerformed(ActionEvent e)
1123   {
1124     Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1125   }
1126
1127   @Override
1128   public void save_actionPerformed(ActionEvent e)
1129   {
1130     if (fileName == null || (currentFileFormat == null)
1131             || fileName.startsWith("http"))
1132     {
1133       saveAs_actionPerformed();
1134     }
1135     else
1136     {
1137       saveAlignment(fileName, currentFileFormat);
1138     }
1139   }
1140
1141   /**
1142    * Saves the alignment to a file with a name chosen by the user, if necessary
1143    * warning if a file would be overwritten
1144    */
1145   @Override
1146   public void saveAs_actionPerformed()
1147   {
1148     String format = currentFileFormat == null ? null
1149             : currentFileFormat.getName();
1150     JalviewFileChooser chooser = JalviewFileChooser
1151             .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1152
1153     chooser.setFileView(new JalviewFileView());
1154     chooser.setDialogTitle(
1155             MessageManager.getString("label.save_alignment_to_file"));
1156     chooser.setToolTipText(MessageManager.getString("action.save"));
1157
1158     int value = chooser.showSaveDialog(this);
1159
1160     if (value != JalviewFileChooser.APPROVE_OPTION)
1161     {
1162       return;
1163     }
1164     currentFileFormat = chooser.getSelectedFormat();
1165     // todo is this (2005) test now obsolete - value is never null?
1166     while (currentFileFormat == null)
1167     {
1168       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1169               MessageManager
1170                       .getString("label.select_file_format_before_saving"),
1171               MessageManager.getString("label.file_format_not_specified"),
1172               JvOptionPane.WARNING_MESSAGE);
1173       currentFileFormat = chooser.getSelectedFormat();
1174       value = chooser.showSaveDialog(this);
1175       if (value != JalviewFileChooser.APPROVE_OPTION)
1176       {
1177         return;
1178       }
1179     }
1180
1181     fileName = chooser.getSelectedFile().getPath();
1182
1183     Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1184     Cache.setProperty("LAST_DIRECTORY", fileName);
1185     saveAlignment(fileName, currentFileFormat);
1186   }
1187
1188   boolean lastSaveSuccessful = false;
1189
1190   FileFormatI lastFormatSaved;
1191
1192   String lastFilenameSaved;
1193
1194   /**
1195    * Raise a dialog or status message for the last call to saveAlignment.
1196    *
1197    * @return true if last call to saveAlignment(file, format) was successful.
1198    */
1199   public boolean isSaveAlignmentSuccessful()
1200   {
1201
1202     if (!lastSaveSuccessful)
1203     {
1204       JvOptionPane.showInternalMessageDialog(this, MessageManager
1205               .formatMessage("label.couldnt_save_file", new Object[]
1206               { lastFilenameSaved }),
1207               MessageManager.getString("label.error_saving_file"),
1208               JvOptionPane.WARNING_MESSAGE);
1209     }
1210     else
1211     {
1212
1213       setStatus(MessageManager.formatMessage(
1214               "label.successfully_saved_to_file_in_format", new Object[]
1215               { lastFilenameSaved, lastFormatSaved }));
1216
1217     }
1218     return lastSaveSuccessful;
1219   }
1220
1221   /**
1222    * Saves the alignment to the specified file path, in the specified format,
1223    * which may be an alignment format, or Jalview project format. If the
1224    * alignment has hidden regions, or the format is one capable of including
1225    * non-sequence data (features, annotations, groups), then the user may be
1226    * prompted to specify what to include in the output.
1227    *
1228    * @param file
1229    * @param format
1230    */
1231   public void saveAlignment(String file, FileFormatI format)
1232   {
1233     lastSaveSuccessful = false;
1234     lastFilenameSaved = file;
1235     lastFormatSaved = format;
1236
1237     if (FileFormat.Jalview.equals(format))
1238     {
1239       String shortName = title;
1240       if (shortName.indexOf(File.separatorChar) > -1)
1241       {
1242         shortName = shortName.substring(
1243                 shortName.lastIndexOf(File.separatorChar) + 1);
1244       }
1245       lastSaveSuccessful = new jalview.project.Jalview2XML().saveAlignment(this, file,
1246               shortName);
1247
1248       statusBar.setText(MessageManager.formatMessage(
1249               "label.successfully_saved_to_file_in_format", new Object[]
1250               { fileName, format }));
1251
1252       return;
1253     }
1254
1255     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1256     Runnable cancelAction = new Runnable()
1257     {
1258       @Override
1259       public void run()
1260       {
1261         lastSaveSuccessful = false;
1262       }
1263     };
1264     Runnable outputAction = new Runnable()
1265     {
1266       @Override
1267       public void run()
1268       {
1269         // todo defer this to inside formatSequences (or later)
1270         AlignmentExportData exportData = viewport
1271                 .getAlignExportData(options);
1272         String output = new FormatAdapter(alignPanel, options)
1273                 .formatSequences(format, exportData.getAlignment(),
1274                         exportData.getOmitHidden(),
1275                         exportData.getStartEndPostions(),
1276                         viewport.getAlignment().getHiddenColumns());
1277         if (output == null)
1278         {
1279           lastSaveSuccessful = false;
1280         }
1281         else
1282         {
1283           try
1284           {
1285             PrintWriter out = new PrintWriter(new FileWriter(file));
1286             out.print(output);
1287             out.close();
1288             AlignFrame.this.setTitle(file);
1289             setStatus(MessageManager.formatMessage(
1290                     "label.successfully_saved_to_file_in_format",
1291                     new Object[]
1292                     { fileName, format.getName() }));
1293           } catch (Exception ex)
1294           {
1295             lastSaveSuccessful = false;
1296             ex.printStackTrace();
1297           }
1298         }
1299       }
1300     };
1301
1302     /*
1303      * show dialog with export options if applicable; else just do it
1304      */
1305     if (AlignExportOptions.isNeeded(viewport, format))
1306     {
1307       AlignExportOptions choices = new AlignExportOptions(
1308               alignPanel.getAlignViewport(), format, options);
1309       choices.setResponseAction(0, outputAction);
1310       choices.setResponseAction(1, cancelAction);
1311       choices.showDialog();
1312     }
1313     else
1314     {
1315       outputAction.run();
1316     }
1317   }
1318
1319   /**
1320    * Outputs the alignment to textbox in the requested format, if necessary
1321    * first prompting the user for whether to include hidden regions or
1322    * non-sequence data
1323    *
1324    * @param fileFormatName
1325    */
1326   @Override
1327   protected void outputText_actionPerformed(String fileFormatName)
1328   {
1329     FileFormatI fileFormat = FileFormats.getInstance()
1330             .forName(fileFormatName);
1331     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1332     Runnable outputAction = new Runnable()
1333     {
1334       @Override
1335       public void run()
1336       {
1337         // todo defer this to inside formatSequences (or later)
1338         AlignmentExportData exportData = viewport
1339                 .getAlignExportData(options);
1340         CutAndPasteTransfer cap = new CutAndPasteTransfer();
1341         cap.setForInput(null);
1342         try
1343         {
1344           FileFormatI format = fileFormat;
1345           cap.setText(new FormatAdapter(alignPanel, options)
1346                   .formatSequences(format, exportData.getAlignment(),
1347                           exportData.getOmitHidden(),
1348                           exportData.getStartEndPostions(),
1349                           viewport.getAlignment().getHiddenColumns()));
1350           Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1351                   "label.alignment_output_command", new Object[]
1352                   { fileFormat.getName() }), 600, 500);
1353         } catch (OutOfMemoryError oom)
1354         {
1355           new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1356                   oom);
1357           cap.dispose();
1358         }
1359       }
1360     };
1361
1362     /*
1363      * show dialog with export options if applicable; else just do it
1364      */
1365     if (AlignExportOptions.isNeeded(viewport, fileFormat))
1366     {
1367       AlignExportOptions choices = new AlignExportOptions(
1368               alignPanel.getAlignViewport(), fileFormat, options);
1369       choices.setResponseAction(0, outputAction);
1370       choices.showDialog();
1371     }
1372     else
1373     {
1374       outputAction.run();
1375     }
1376   }
1377
1378   /**
1379    * DOCUMENT ME!
1380    *
1381    * @param e
1382    *          DOCUMENT ME!
1383    */
1384   @Override
1385   protected void htmlMenuItem_actionPerformed(ActionEvent e)
1386   {
1387     HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1388     htmlSVG.exportHTML(null);
1389   }
1390
1391   @Override
1392   public void bioJSMenuItem_actionPerformed(ActionEvent e)
1393   {
1394     BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1395     bjs.exportHTML(null);
1396   }
1397
1398   public void createImageMap(File file, String image)
1399   {
1400     alignPanel.makePNGImageMap(file, image);
1401   }
1402
1403   /**
1404    * Creates a PNG image of the alignment and writes it to the given file. If
1405    * the file is null, the user is prompted to choose a file.
1406    *
1407    * @param f
1408    */
1409   @Override
1410   public void createPNG(File f)
1411   {
1412     alignPanel.makeAlignmentImage(TYPE.PNG, f);
1413   }
1414
1415   /**
1416    * Creates an EPS image of the alignment and writes it to the given file. If
1417    * the file is null, the user is prompted to choose a file.
1418    *
1419    * @param f
1420    */
1421   @Override
1422   public void createEPS(File f)
1423   {
1424     alignPanel.makeAlignmentImage(TYPE.EPS, f);
1425   }
1426
1427   /**
1428    * Creates an SVG image of the alignment and writes it to the given file. If
1429    * the file is null, the user is prompted to choose a file.
1430    *
1431    * @param f
1432    */
1433   @Override
1434   public void createSVG(File f)
1435   {
1436     alignPanel.makeAlignmentImage(TYPE.SVG, f);
1437   }
1438
1439   @Override
1440   public void pageSetup_actionPerformed(ActionEvent e)
1441   {
1442     PrinterJob printJob = PrinterJob.getPrinterJob();
1443     PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1444   }
1445
1446   /**
1447    * DOCUMENT ME!
1448    *
1449    * @param e
1450    *          DOCUMENT ME!
1451    */
1452   @Override
1453   public void printMenuItem_actionPerformed(ActionEvent e)
1454   {
1455     // Putting in a thread avoids Swing painting problems
1456     PrintThread thread = new PrintThread(alignPanel);
1457     thread.start();
1458   }
1459
1460   @Override
1461   public void exportFeatures_actionPerformed(ActionEvent e)
1462   {
1463     new AnnotationExporter(alignPanel).exportFeatures();
1464   }
1465
1466   @Override
1467   public void exportAnnotations_actionPerformed(ActionEvent e)
1468   {
1469     new AnnotationExporter(alignPanel).exportAnnotations();
1470   }
1471
1472   @Override
1473   public void associatedData_actionPerformed(ActionEvent e)
1474   {
1475     final JalviewFileChooser chooser = new JalviewFileChooser(
1476             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1477     chooser.setFileView(new JalviewFileView());
1478     chooser.setDialogTitle(
1479             MessageManager.getString("label.load_jalview_annotations"));
1480     chooser.setToolTipText(
1481             MessageManager.getString("label.load_jalview_annotations"));
1482     chooser.setResponseHandler(0, new Runnable()
1483     {
1484       @Override
1485       public void run()
1486       {
1487         String choice = chooser.getSelectedFile().getPath();
1488         jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1489         loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1490       }
1491     });
1492
1493     chooser.showOpenDialog(this);
1494   }
1495
1496   /**
1497    * Close the current view or all views in the alignment frame. If the frame
1498    * only contains one view then the alignment will be removed from memory.
1499    *
1500    * @param closeAllTabs
1501    */
1502   @Override
1503   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1504   {
1505     if (alignPanels != null && alignPanels.size() < 2)
1506     {
1507       closeAllTabs = true;
1508     }
1509
1510     try
1511     {
1512       if (alignPanels != null)
1513       {
1514         if (closeAllTabs)
1515         {
1516           if (this.isClosed())
1517           {
1518             // really close all the windows - otherwise wait till
1519             // setClosed(true) is called
1520             for (int i = 0; i < alignPanels.size(); i++)
1521             {
1522               AlignmentPanel ap = alignPanels.get(i);
1523               ap.closePanel();
1524             }
1525           }
1526         }
1527         else
1528         {
1529           closeView(alignPanel);
1530         }
1531       }
1532
1533       if (closeAllTabs)
1534       {
1535         /*
1536          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1537          * be called recursively, with the frame now in 'closed' state
1538          */
1539         this.setClosed(true);
1540       }
1541     } catch (Exception ex)
1542     {
1543       ex.printStackTrace();
1544     }
1545   }
1546
1547   /**
1548    * Close the specified panel and close up tabs appropriately.
1549    *
1550    * @param panelToClose
1551    */
1552   public void closeView(AlignmentPanel panelToClose)
1553   {
1554     int index = tabbedPane.getSelectedIndex();
1555     int closedindex = tabbedPane.indexOfComponent(panelToClose);
1556     alignPanels.remove(panelToClose);
1557     panelToClose.closePanel();
1558     panelToClose = null;
1559
1560     tabbedPane.removeTabAt(closedindex);
1561     tabbedPane.validate();
1562
1563     if (index > closedindex || index == tabbedPane.getTabCount())
1564     {
1565       // modify currently selected tab index if necessary.
1566       index--;
1567     }
1568
1569     this.tabSelectionChanged(index);
1570   }
1571
1572   /**
1573    * DOCUMENT ME!
1574    */
1575   void updateEditMenuBar()
1576   {
1577
1578     if (viewport.getHistoryList().size() > 0)
1579     {
1580       undoMenuItem.setEnabled(true);
1581       CommandI command = viewport.getHistoryList().peek();
1582       undoMenuItem.setText(MessageManager
1583               .formatMessage("label.undo_command", new Object[]
1584               { command.getDescription() }));
1585     }
1586     else
1587     {
1588       undoMenuItem.setEnabled(false);
1589       undoMenuItem.setText(MessageManager.getString("action.undo"));
1590     }
1591
1592     if (viewport.getRedoList().size() > 0)
1593     {
1594       redoMenuItem.setEnabled(true);
1595
1596       CommandI command = viewport.getRedoList().peek();
1597       redoMenuItem.setText(MessageManager
1598               .formatMessage("label.redo_command", new Object[]
1599               { command.getDescription() }));
1600     }
1601     else
1602     {
1603       redoMenuItem.setEnabled(false);
1604       redoMenuItem.setText(MessageManager.getString("action.redo"));
1605     }
1606   }
1607
1608   @Override
1609   public void addHistoryItem(CommandI command)
1610   {
1611     if (command.getSize() > 0)
1612     {
1613       viewport.addToHistoryList(command);
1614       viewport.clearRedoList();
1615       updateEditMenuBar();
1616       viewport.updateHiddenColumns();
1617       // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1618       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1619       // viewport.getColumnSelection()
1620       // .getHiddenColumns().size() > 0);
1621     }
1622   }
1623
1624   /**
1625    *
1626    * @return alignment objects for all views
1627    */
1628   AlignmentI[] getViewAlignments()
1629   {
1630     if (alignPanels != null)
1631     {
1632       AlignmentI[] als = new AlignmentI[alignPanels.size()];
1633       int i = 0;
1634       for (AlignmentPanel ap : alignPanels)
1635       {
1636         als[i++] = ap.av.getAlignment();
1637       }
1638       return als;
1639     }
1640     if (viewport != null)
1641     {
1642       return new AlignmentI[] { viewport.getAlignment() };
1643     }
1644     return null;
1645   }
1646
1647   /**
1648    * DOCUMENT ME!
1649    *
1650    * @param e
1651    *          DOCUMENT ME!
1652    */
1653   @Override
1654   protected void undoMenuItem_actionPerformed(ActionEvent e)
1655   {
1656     if (viewport.getHistoryList().isEmpty())
1657     {
1658       return;
1659     }
1660     CommandI command = viewport.getHistoryList().pop();
1661     viewport.addToRedoList(command);
1662     command.undoCommand(getViewAlignments());
1663
1664     AlignmentViewport originalSource = getOriginatingSource(command);
1665     updateEditMenuBar();
1666
1667     if (originalSource != null)
1668     {
1669       if (originalSource != viewport)
1670       {
1671         Cache.log.warn(
1672                 "Implementation worry: mismatch of viewport origin for undo");
1673       }
1674       originalSource.updateHiddenColumns();
1675       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1676       // null
1677       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1678       // viewport.getColumnSelection()
1679       // .getHiddenColumns().size() > 0);
1680       originalSource.firePropertyChange("alignment", null,
1681               originalSource.getAlignment().getSequences());
1682     }
1683   }
1684
1685   /**
1686    * DOCUMENT ME!
1687    *
1688    * @param e
1689    *          DOCUMENT ME!
1690    */
1691   @Override
1692   protected void redoMenuItem_actionPerformed(ActionEvent e)
1693   {
1694     if (viewport.getRedoList().size() < 1)
1695     {
1696       return;
1697     }
1698
1699     CommandI command = viewport.getRedoList().pop();
1700     viewport.addToHistoryList(command);
1701     command.doCommand(getViewAlignments());
1702
1703     AlignmentViewport originalSource = getOriginatingSource(command);
1704     updateEditMenuBar();
1705
1706     if (originalSource != null)
1707     {
1708
1709       if (originalSource != viewport)
1710       {
1711         Cache.log.warn(
1712                 "Implementation worry: mismatch of viewport origin for redo");
1713       }
1714       originalSource.updateHiddenColumns();
1715       // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1716       // null
1717       // && viewport.getColumnSelection().getHiddenColumns() != null &&
1718       // viewport.getColumnSelection()
1719       // .getHiddenColumns().size() > 0);
1720       originalSource.firePropertyChange("alignment", null,
1721               originalSource.getAlignment().getSequences());
1722     }
1723   }
1724
1725   AlignmentViewport getOriginatingSource(CommandI command)
1726   {
1727     AlignmentViewport originalSource = null;
1728     // For sequence removal and addition, we need to fire
1729     // the property change event FROM the viewport where the
1730     // original alignment was altered
1731     AlignmentI al = null;
1732     if (command instanceof EditCommand)
1733     {
1734       EditCommand editCommand = (EditCommand) command;
1735       al = editCommand.getAlignment();
1736       List<Component> comps = PaintRefresher.components
1737               .get(viewport.getSequenceSetId());
1738
1739       for (Component comp : comps)
1740       {
1741         if (comp instanceof AlignmentPanel)
1742         {
1743           if (al == ((AlignmentPanel) comp).av.getAlignment())
1744           {
1745             originalSource = ((AlignmentPanel) comp).av;
1746             break;
1747           }
1748         }
1749       }
1750     }
1751
1752     if (originalSource == null)
1753     {
1754       // The original view is closed, we must validate
1755       // the current view against the closed view first
1756       if (al != null)
1757       {
1758         PaintRefresher.validateSequences(al, viewport.getAlignment());
1759       }
1760
1761       originalSource = viewport;
1762     }
1763
1764     return originalSource;
1765   }
1766
1767   /**
1768    * DOCUMENT ME!
1769    *
1770    * @param up
1771    *          DOCUMENT ME!
1772    */
1773   public void moveSelectedSequences(boolean up)
1774   {
1775     SequenceGroup sg = viewport.getSelectionGroup();
1776
1777     if (sg == null)
1778     {
1779       return;
1780     }
1781     viewport.getAlignment().moveSelectedSequencesByOne(sg,
1782             viewport.getHiddenRepSequences(), up);
1783     alignPanel.paintAlignment(true, false);
1784   }
1785
1786   synchronized void slideSequences(boolean right, int size)
1787   {
1788     List<SequenceI> sg = new ArrayList<>();
1789     if (viewport.cursorMode)
1790     {
1791       sg.add(viewport.getAlignment()
1792               .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1793     }
1794     else if (viewport.getSelectionGroup() != null
1795             && viewport.getSelectionGroup().getSize() != viewport
1796                     .getAlignment().getHeight())
1797     {
1798       sg = viewport.getSelectionGroup()
1799               .getSequences(viewport.getHiddenRepSequences());
1800     }
1801
1802     if (sg.size() < 1)
1803     {
1804       return;
1805     }
1806
1807     List<SequenceI> invertGroup = new ArrayList<>();
1808
1809     for (SequenceI seq : viewport.getAlignment().getSequences())
1810     {
1811       if (!sg.contains(seq))
1812       {
1813         invertGroup.add(seq);
1814       }
1815     }
1816
1817     SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1818
1819     SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1820     for (int i = 0; i < invertGroup.size(); i++)
1821     {
1822       seqs2[i] = invertGroup.get(i);
1823     }
1824
1825     SlideSequencesCommand ssc;
1826     if (right)
1827     {
1828       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1829               viewport.getGapCharacter());
1830     }
1831     else
1832     {
1833       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1834               viewport.getGapCharacter());
1835     }
1836
1837     int groupAdjustment = 0;
1838     if (ssc.getGapsInsertedBegin() && right)
1839     {
1840       if (viewport.cursorMode)
1841       {
1842         alignPanel.getSeqPanel().moveCursor(size, 0);
1843       }
1844       else
1845       {
1846         groupAdjustment = size;
1847       }
1848     }
1849     else if (!ssc.getGapsInsertedBegin() && !right)
1850     {
1851       if (viewport.cursorMode)
1852       {
1853         alignPanel.getSeqPanel().moveCursor(-size, 0);
1854       }
1855       else
1856       {
1857         groupAdjustment = -size;
1858       }
1859     }
1860
1861     if (groupAdjustment != 0)
1862     {
1863       viewport.getSelectionGroup().setStartRes(
1864               viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1865       viewport.getSelectionGroup().setEndRes(
1866               viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1867     }
1868
1869     /*
1870      * just extend the last slide command if compatible; but not if in
1871      * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1872      */
1873     boolean appendHistoryItem = false;
1874     Deque<CommandI> historyList = viewport.getHistoryList();
1875     boolean inSplitFrame = getSplitViewContainer() != null;
1876     if (!inSplitFrame && historyList != null && historyList.size() > 0
1877             && historyList.peek() instanceof SlideSequencesCommand)
1878     {
1879       appendHistoryItem = ssc.appendSlideCommand(
1880               (SlideSequencesCommand) historyList.peek());
1881     }
1882
1883     if (!appendHistoryItem)
1884     {
1885       addHistoryItem(ssc);
1886     }
1887
1888     repaint();
1889   }
1890
1891   /**
1892    * DOCUMENT ME!
1893    *
1894    * @param e
1895    *          DOCUMENT ME!
1896    */
1897   @Override
1898   protected void copy_actionPerformed(ActionEvent e)
1899   {
1900     if (viewport.getSelectionGroup() == null)
1901     {
1902       return;
1903     }
1904     // TODO: preserve the ordering of displayed alignment annotation in any
1905     // internal paste (particularly sequence associated annotation)
1906     SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1907     String[] omitHidden = null;
1908
1909     if (viewport.hasHiddenColumns())
1910     {
1911       omitHidden = viewport.getViewAsString(true);
1912     }
1913
1914     String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1915             seqs, omitHidden, null);
1916
1917     StringSelection ss = new StringSelection(output);
1918
1919     try
1920     {
1921       jalview.gui.Desktop.internalCopy = true;
1922       // Its really worth setting the clipboard contents
1923       // to empty before setting the large StringSelection!!
1924       Toolkit.getDefaultToolkit().getSystemClipboard()
1925               .setContents(new StringSelection(""), null);
1926
1927       Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1928               Desktop.instance);
1929     } catch (OutOfMemoryError er)
1930     {
1931       new OOMWarning("copying region", er);
1932       return;
1933     }
1934
1935     HiddenColumns hiddenColumns = null;
1936     if (viewport.hasHiddenColumns())
1937     {
1938       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1939       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1940
1941       // create new HiddenColumns object with copy of hidden regions
1942       // between startRes and endRes, offset by startRes
1943       hiddenColumns = new HiddenColumns(
1944               viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1945               hiddenCutoff, hiddenOffset);
1946     }
1947
1948     Desktop.jalviewClipboard = new Object[] { seqs,
1949         viewport.getAlignment().getDataset(), hiddenColumns };
1950     setStatus(MessageManager.formatMessage(
1951             "label.copied_sequences_to_clipboard", new Object[]
1952             { Integer.valueOf(seqs.length).toString() }));
1953   }
1954
1955   /**
1956    * DOCUMENT ME!
1957    *
1958    * @param e
1959    *          DOCUMENT ME!
1960    */
1961   @Override
1962   protected void pasteNew_actionPerformed(ActionEvent e)
1963   {
1964     paste(true);
1965   }
1966
1967   /**
1968    * DOCUMENT ME!
1969    *
1970    * @param e
1971    *          DOCUMENT ME!
1972    */
1973   @Override
1974   protected void pasteThis_actionPerformed(ActionEvent e)
1975   {
1976     paste(false);
1977   }
1978
1979   /**
1980    * Paste contents of Jalview clipboard
1981    *
1982    * @param newAlignment
1983    *          true to paste to a new alignment, otherwise add to this.
1984    */
1985   void paste(boolean newAlignment)
1986   {
1987     boolean externalPaste = true;
1988     try
1989     {
1990       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
1991       Transferable contents = c.getContents(this);
1992
1993       if (contents == null)
1994       {
1995         return;
1996       }
1997
1998       String str;
1999       FileFormatI format;
2000       try
2001       {
2002         str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2003         if (str.length() < 1)
2004         {
2005           return;
2006         }
2007
2008         format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2009
2010       } catch (OutOfMemoryError er)
2011       {
2012         new OOMWarning("Out of memory pasting sequences!!", er);
2013         return;
2014       }
2015
2016       SequenceI[] sequences;
2017       boolean annotationAdded = false;
2018       AlignmentI alignment = null;
2019
2020       if (Desktop.jalviewClipboard != null)
2021       {
2022         // The clipboard was filled from within Jalview, we must use the
2023         // sequences
2024         // And dataset from the copied alignment
2025         SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2026         // be doubly sure that we create *new* sequence objects.
2027         sequences = new SequenceI[newseq.length];
2028         for (int i = 0; i < newseq.length; i++)
2029         {
2030           sequences[i] = new Sequence(newseq[i]);
2031         }
2032         alignment = new Alignment(sequences);
2033         externalPaste = false;
2034       }
2035       else
2036       {
2037         // parse the clipboard as an alignment.
2038         alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2039                 format);
2040         sequences = alignment.getSequencesArray();
2041       }
2042
2043       int alwidth = 0;
2044       ArrayList<Integer> newGraphGroups = new ArrayList<>();
2045       int fgroup = -1;
2046
2047       if (newAlignment)
2048       {
2049
2050         if (Desktop.jalviewClipboard != null)
2051         {
2052           // dataset is inherited
2053           alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2054         }
2055         else
2056         {
2057           // new dataset is constructed
2058           alignment.setDataset(null);
2059         }
2060         alwidth = alignment.getWidth() + 1;
2061       }
2062       else
2063       {
2064         AlignmentI pastedal = alignment; // preserve pasted alignment object
2065         // Add pasted sequences and dataset into existing alignment.
2066         alignment = viewport.getAlignment();
2067         alwidth = alignment.getWidth() + 1;
2068         // decide if we need to import sequences from an existing dataset
2069         boolean importDs = Desktop.jalviewClipboard != null
2070                 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2071         // importDs==true instructs us to copy over new dataset sequences from
2072         // an existing alignment
2073         Vector newDs = (importDs) ? new Vector() : null; // used to create
2074         // minimum dataset set
2075
2076         for (int i = 0; i < sequences.length; i++)
2077         {
2078           if (importDs)
2079           {
2080             newDs.addElement(null);
2081           }
2082           SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2083           // paste
2084           if (importDs && ds != null)
2085           {
2086             if (!newDs.contains(ds))
2087             {
2088               newDs.setElementAt(ds, i);
2089               ds = new Sequence(ds);
2090               // update with new dataset sequence
2091               sequences[i].setDatasetSequence(ds);
2092             }
2093             else
2094             {
2095               ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2096             }
2097           }
2098           else
2099           {
2100             // copy and derive new dataset sequence
2101             sequences[i] = sequences[i].deriveSequence();
2102             alignment.getDataset()
2103                     .addSequence(sequences[i].getDatasetSequence());
2104             // TODO: avoid creation of duplicate dataset sequences with a
2105             // 'contains' method using SequenceI.equals()/SequenceI.contains()
2106           }
2107           alignment.addSequence(sequences[i]); // merges dataset
2108         }
2109         if (newDs != null)
2110         {
2111           newDs.clear(); // tidy up
2112         }
2113         if (alignment.getAlignmentAnnotation() != null)
2114         {
2115           for (AlignmentAnnotation alan : alignment
2116                   .getAlignmentAnnotation())
2117           {
2118             if (alan.graphGroup > fgroup)
2119             {
2120               fgroup = alan.graphGroup;
2121             }
2122           }
2123         }
2124         if (pastedal.getAlignmentAnnotation() != null)
2125         {
2126           // Add any annotation attached to alignment.
2127           AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2128           for (int i = 0; i < alann.length; i++)
2129           {
2130             annotationAdded = true;
2131             if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2132             {
2133               AlignmentAnnotation newann = new AlignmentAnnotation(
2134                       alann[i]);
2135               if (newann.graphGroup > -1)
2136               {
2137                 if (newGraphGroups.size() <= newann.graphGroup
2138                         || newGraphGroups.get(newann.graphGroup) == null)
2139                 {
2140                   for (int q = newGraphGroups
2141                           .size(); q <= newann.graphGroup; q++)
2142                   {
2143                     newGraphGroups.add(q, null);
2144                   }
2145                   newGraphGroups.set(newann.graphGroup,
2146                           new Integer(++fgroup));
2147                 }
2148                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2149                         .intValue();
2150               }
2151
2152               newann.padAnnotation(alwidth);
2153               alignment.addAnnotation(newann);
2154             }
2155           }
2156         }
2157       }
2158       if (!newAlignment)
2159       {
2160         // /////
2161         // ADD HISTORY ITEM
2162         //
2163         addHistoryItem(new EditCommand(
2164                 MessageManager.getString("label.add_sequences"),
2165                 Action.PASTE, sequences, 0, alignment.getWidth(),
2166                 alignment));
2167       }
2168       // Add any annotations attached to sequences
2169       for (int i = 0; i < sequences.length; i++)
2170       {
2171         if (sequences[i].getAnnotation() != null)
2172         {
2173           AlignmentAnnotation newann;
2174           for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2175           {
2176             annotationAdded = true;
2177             newann = sequences[i].getAnnotation()[a];
2178             newann.adjustForAlignment();
2179             newann.padAnnotation(alwidth);
2180             if (newann.graphGroup > -1)
2181             {
2182               if (newann.graphGroup > -1)
2183               {
2184                 if (newGraphGroups.size() <= newann.graphGroup
2185                         || newGraphGroups.get(newann.graphGroup) == null)
2186                 {
2187                   for (int q = newGraphGroups
2188                           .size(); q <= newann.graphGroup; q++)
2189                   {
2190                     newGraphGroups.add(q, null);
2191                   }
2192                   newGraphGroups.set(newann.graphGroup,
2193                           new Integer(++fgroup));
2194                 }
2195                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2196                         .intValue();
2197               }
2198             }
2199             alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2200             // was
2201             // duplicated
2202             // earlier
2203             alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2204                     a);
2205           }
2206         }
2207       }
2208       if (!newAlignment)
2209       {
2210
2211         // propagate alignment changed.
2212         viewport.getRanges().setEndSeq(alignment.getHeight());
2213         if (annotationAdded)
2214         {
2215           // Duplicate sequence annotation in all views.
2216           AlignmentI[] alview = this.getViewAlignments();
2217           for (int i = 0; i < sequences.length; i++)
2218           {
2219             AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2220             if (sann == null)
2221             {
2222               continue;
2223             }
2224             for (int avnum = 0; avnum < alview.length; avnum++)
2225             {
2226               if (alview[avnum] != alignment)
2227               {
2228                 // duplicate in a view other than the one with input focus
2229                 int avwidth = alview[avnum].getWidth() + 1;
2230                 // this relies on sann being preserved after we
2231                 // modify the sequence's annotation array for each duplication
2232                 for (int a = 0; a < sann.length; a++)
2233                 {
2234                   AlignmentAnnotation newann = new AlignmentAnnotation(
2235                           sann[a]);
2236                   sequences[i].addAlignmentAnnotation(newann);
2237                   newann.padAnnotation(avwidth);
2238                   alview[avnum].addAnnotation(newann); // annotation was
2239                   // duplicated earlier
2240                   // TODO JAL-1145 graphGroups are not updated for sequence
2241                   // annotation added to several views. This may cause
2242                   // strangeness
2243                   alview[avnum].setAnnotationIndex(newann, a);
2244                 }
2245               }
2246             }
2247           }
2248           buildSortByAnnotationScoresMenu();
2249         }
2250         viewport.firePropertyChange("alignment", null,
2251                 alignment.getSequences());
2252         if (alignPanels != null)
2253         {
2254           for (AlignmentPanel ap : alignPanels)
2255           {
2256             ap.validateAnnotationDimensions(false);
2257           }
2258         }
2259         else
2260         {
2261           alignPanel.validateAnnotationDimensions(false);
2262         }
2263
2264       }
2265       else
2266       {
2267         AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2268                 DEFAULT_HEIGHT);
2269         String newtitle = new String("Copied sequences");
2270
2271         if (Desktop.jalviewClipboard != null
2272                 && Desktop.jalviewClipboard[2] != null)
2273         {
2274           HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2275           af.viewport.setHiddenColumns(hc);
2276         }
2277
2278         // >>>This is a fix for the moment, until a better solution is
2279         // found!!<<<
2280         af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2281                 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2282                         .getFeatureRenderer());
2283
2284         // TODO: maintain provenance of an alignment, rather than just make the
2285         // title a concatenation of operations.
2286         if (!externalPaste)
2287         {
2288           if (title.startsWith("Copied sequences"))
2289           {
2290             newtitle = title;
2291           }
2292           else
2293           {
2294             newtitle = newtitle.concat("- from " + title);
2295           }
2296         }
2297         else
2298         {
2299           newtitle = new String("Pasted sequences");
2300         }
2301
2302         Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2303                 DEFAULT_HEIGHT);
2304
2305       }
2306
2307     } catch (Exception ex)
2308     {
2309       ex.printStackTrace();
2310       System.out.println("Exception whilst pasting: " + ex);
2311       // could be anything being pasted in here
2312     }
2313
2314   }
2315
2316   @Override
2317   protected void expand_newalign(ActionEvent e)
2318   {
2319     try
2320     {
2321       AlignmentI alignment = AlignmentUtils
2322               .expandContext(getViewport().getAlignment(), -1);
2323       AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2324               DEFAULT_HEIGHT);
2325       String newtitle = new String("Flanking alignment");
2326
2327       if (Desktop.jalviewClipboard != null
2328               && Desktop.jalviewClipboard[2] != null)
2329       {
2330         HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2331         af.viewport.setHiddenColumns(hc);
2332       }
2333
2334       // >>>This is a fix for the moment, until a better solution is
2335       // found!!<<<
2336       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2337               .transferSettings(alignPanel.getSeqPanel().seqCanvas
2338                       .getFeatureRenderer());
2339
2340       // TODO: maintain provenance of an alignment, rather than just make the
2341       // title a concatenation of operations.
2342       {
2343         if (title.startsWith("Copied sequences"))
2344         {
2345           newtitle = title;
2346         }
2347         else
2348         {
2349           newtitle = newtitle.concat("- from " + title);
2350         }
2351       }
2352
2353       Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2354
2355     } catch (Exception ex)
2356     {
2357       ex.printStackTrace();
2358       System.out.println("Exception whilst pasting: " + ex);
2359       // could be anything being pasted in here
2360     } catch (OutOfMemoryError oom)
2361     {
2362       new OOMWarning("Viewing flanking region of alignment", oom);
2363     }
2364   }
2365
2366   /**
2367    * DOCUMENT ME!
2368    *
2369    * @param e
2370    *          DOCUMENT ME!
2371    */
2372   @Override
2373   protected void cut_actionPerformed(ActionEvent e)
2374   {
2375     copy_actionPerformed(null);
2376     delete_actionPerformed(null);
2377   }
2378
2379   /**
2380    * DOCUMENT ME!
2381    *
2382    * @param e
2383    *          DOCUMENT ME!
2384    */
2385   @Override
2386   protected void delete_actionPerformed(ActionEvent evt)
2387   {
2388
2389     SequenceGroup sg = viewport.getSelectionGroup();
2390     if (sg == null)
2391     {
2392       return;
2393     }
2394
2395     /*
2396      * If the cut affects all sequences, warn, remove highlighted columns
2397      */
2398     if (sg.getSize() == viewport.getAlignment().getHeight())
2399     {
2400       boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
2401               + 1) == viewport.getAlignment().getWidth()) ? true : false;
2402       if (isEntireAlignWidth)
2403       {
2404         int confirm = JvOptionPane.showConfirmDialog(this,
2405                 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2406                 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2407                 JvOptionPane.OK_CANCEL_OPTION);
2408
2409         if (confirm == JvOptionPane.CANCEL_OPTION
2410                 || confirm == JvOptionPane.CLOSED_OPTION)
2411         {
2412           return;
2413         }
2414       }
2415       viewport.getColumnSelection().removeElements(sg.getStartRes(),
2416               sg.getEndRes() + 1);
2417     }
2418     SequenceI[] cut = sg.getSequences()
2419             .toArray(new SequenceI[sg.getSize()]);
2420
2421     addHistoryItem(new EditCommand(
2422             MessageManager.getString("label.cut_sequences"), Action.CUT,
2423             cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2424             viewport.getAlignment()));
2425
2426     viewport.setSelectionGroup(null);
2427     viewport.sendSelection();
2428     viewport.getAlignment().deleteGroup(sg);
2429
2430     viewport.firePropertyChange("alignment", null,
2431             viewport.getAlignment().getSequences());
2432     if (viewport.getAlignment().getHeight() < 1)
2433     {
2434       try
2435       {
2436         this.setClosed(true);
2437       } catch (Exception ex)
2438       {
2439       }
2440     }
2441   }
2442
2443   /**
2444    * DOCUMENT ME!
2445    *
2446    * @param e
2447    *          DOCUMENT ME!
2448    */
2449   @Override
2450   protected void deleteGroups_actionPerformed(ActionEvent e)
2451   {
2452     if (avc.deleteGroups())
2453     {
2454       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2455       alignPanel.updateAnnotation();
2456       alignPanel.paintAlignment(true, true);
2457     }
2458   }
2459
2460   /**
2461    * DOCUMENT ME!
2462    *
2463    * @param e
2464    *          DOCUMENT ME!
2465    */
2466   @Override
2467   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2468   {
2469     SequenceGroup sg = new SequenceGroup();
2470
2471     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2472     {
2473       sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2474     }
2475
2476     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2477     viewport.setSelectionGroup(sg);
2478     viewport.sendSelection();
2479     // JAL-2034 - should delegate to
2480     // alignPanel to decide if overview needs
2481     // updating.
2482     alignPanel.paintAlignment(false, false);
2483     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2484   }
2485
2486   /**
2487    * DOCUMENT ME!
2488    *
2489    * @param e
2490    *          DOCUMENT ME!
2491    */
2492   @Override
2493   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2494   {
2495     if (viewport.cursorMode)
2496     {
2497       alignPanel.getSeqPanel().keyboardNo1 = null;
2498       alignPanel.getSeqPanel().keyboardNo2 = null;
2499     }
2500     viewport.setSelectionGroup(null);
2501     viewport.getColumnSelection().clear();
2502     viewport.setSelectionGroup(null);
2503     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2504     // JAL-2034 - should delegate to
2505     // alignPanel to decide if overview needs
2506     // updating.
2507     alignPanel.paintAlignment(false, false);
2508     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2509     viewport.sendSelection();
2510   }
2511
2512   /**
2513    * DOCUMENT ME!
2514    *
2515    * @param e
2516    *          DOCUMENT ME!
2517    */
2518   @Override
2519   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2520   {
2521     SequenceGroup sg = viewport.getSelectionGroup();
2522
2523     if (sg == null)
2524     {
2525       selectAllSequenceMenuItem_actionPerformed(null);
2526
2527       return;
2528     }
2529
2530     for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2531     {
2532       sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2533     }
2534     // JAL-2034 - should delegate to
2535     // alignPanel to decide if overview needs
2536     // updating.
2537
2538     alignPanel.paintAlignment(true, false);
2539     PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2540     viewport.sendSelection();
2541   }
2542
2543   @Override
2544   public void invertColSel_actionPerformed(ActionEvent e)
2545   {
2546     viewport.invertColumnSelection();
2547     alignPanel.paintAlignment(true, false);
2548     viewport.sendSelection();
2549   }
2550
2551   /**
2552    * DOCUMENT ME!
2553    *
2554    * @param e
2555    *          DOCUMENT ME!
2556    */
2557   @Override
2558   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2559   {
2560     trimAlignment(true);
2561   }
2562
2563   /**
2564    * DOCUMENT ME!
2565    *
2566    * @param e
2567    *          DOCUMENT ME!
2568    */
2569   @Override
2570   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2571   {
2572     trimAlignment(false);
2573   }
2574
2575   void trimAlignment(boolean trimLeft)
2576   {
2577     ColumnSelection colSel = viewport.getColumnSelection();
2578     int column;
2579
2580     if (!colSel.isEmpty())
2581     {
2582       if (trimLeft)
2583       {
2584         column = colSel.getMin();
2585       }
2586       else
2587       {
2588         column = colSel.getMax();
2589       }
2590
2591       SequenceI[] seqs;
2592       if (viewport.getSelectionGroup() != null)
2593       {
2594         seqs = viewport.getSelectionGroup()
2595                 .getSequencesAsArray(viewport.getHiddenRepSequences());
2596       }
2597       else
2598       {
2599         seqs = viewport.getAlignment().getSequencesArray();
2600       }
2601
2602       TrimRegionCommand trimRegion;
2603       if (trimLeft)
2604       {
2605         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2606                 column, viewport.getAlignment());
2607         viewport.getRanges().setStartRes(0);
2608       }
2609       else
2610       {
2611         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2612                 column, viewport.getAlignment());
2613       }
2614
2615       setStatus(MessageManager
2616               .formatMessage("label.removed_columns", new String[]
2617               { Integer.valueOf(trimRegion.getSize()).toString() }));
2618
2619       addHistoryItem(trimRegion);
2620
2621       for (SequenceGroup sg : viewport.getAlignment().getGroups())
2622       {
2623         if ((trimLeft && !sg.adjustForRemoveLeft(column))
2624                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2625         {
2626           viewport.getAlignment().deleteGroup(sg);
2627         }
2628       }
2629
2630       viewport.firePropertyChange("alignment", null,
2631               viewport.getAlignment().getSequences());
2632     }
2633   }
2634
2635   /**
2636    * DOCUMENT ME!
2637    *
2638    * @param e
2639    *          DOCUMENT ME!
2640    */
2641   @Override
2642   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2643   {
2644     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2645
2646     SequenceI[] seqs;
2647     if (viewport.getSelectionGroup() != null)
2648     {
2649       seqs = viewport.getSelectionGroup()
2650               .getSequencesAsArray(viewport.getHiddenRepSequences());
2651       start = viewport.getSelectionGroup().getStartRes();
2652       end = viewport.getSelectionGroup().getEndRes();
2653     }
2654     else
2655     {
2656       seqs = viewport.getAlignment().getSequencesArray();
2657     }
2658
2659     RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2660             "Remove Gapped Columns", seqs, start, end,
2661             viewport.getAlignment());
2662
2663     addHistoryItem(removeGapCols);
2664
2665     setStatus(MessageManager
2666             .formatMessage("label.removed_empty_columns", new Object[]
2667             { Integer.valueOf(removeGapCols.getSize()).toString() }));
2668
2669     // This is to maintain viewport position on first residue
2670     // of first sequence
2671     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2672     ViewportRanges ranges = viewport.getRanges();
2673     int startRes = seq.findPosition(ranges.getStartRes());
2674     // ShiftList shifts;
2675     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2676     // edit.alColumnChanges=shifts.getInverse();
2677     // if (viewport.hasHiddenColumns)
2678     // viewport.getColumnSelection().compensateForEdits(shifts);
2679     ranges.setStartRes(seq.findIndex(startRes) - 1);
2680     viewport.firePropertyChange("alignment", null,
2681             viewport.getAlignment().getSequences());
2682
2683   }
2684
2685   /**
2686    * DOCUMENT ME!
2687    *
2688    * @param e
2689    *          DOCUMENT ME!
2690    */
2691   @Override
2692   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2693   {
2694     int start = 0, end = viewport.getAlignment().getWidth() - 1;
2695
2696     SequenceI[] seqs;
2697     if (viewport.getSelectionGroup() != null)
2698     {
2699       seqs = viewport.getSelectionGroup()
2700               .getSequencesAsArray(viewport.getHiddenRepSequences());
2701       start = viewport.getSelectionGroup().getStartRes();
2702       end = viewport.getSelectionGroup().getEndRes();
2703     }
2704     else
2705     {
2706       seqs = viewport.getAlignment().getSequencesArray();
2707     }
2708
2709     // This is to maintain viewport position on first residue
2710     // of first sequence
2711     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2712     int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2713
2714     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2715             viewport.getAlignment()));
2716
2717     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2718
2719     viewport.firePropertyChange("alignment", null,
2720             viewport.getAlignment().getSequences());
2721
2722   }
2723
2724   /**
2725    * DOCUMENT ME!
2726    *
2727    * @param e
2728    *          DOCUMENT ME!
2729    */
2730   @Override
2731   public void padGapsMenuitem_actionPerformed(ActionEvent e)
2732   {
2733     viewport.setPadGaps(padGapsMenuitem.isSelected());
2734     viewport.firePropertyChange("alignment", null,
2735             viewport.getAlignment().getSequences());
2736   }
2737
2738   /**
2739    * DOCUMENT ME!
2740    *
2741    * @param e
2742    *          DOCUMENT ME!
2743    */
2744   @Override
2745   public void findMenuItem_actionPerformed(ActionEvent e)
2746   {
2747     new Finder();
2748   }
2749
2750   /**
2751    * Create a new view of the current alignment.
2752    */
2753   @Override
2754   public void newView_actionPerformed(ActionEvent e)
2755   {
2756     newView(null, true);
2757   }
2758
2759   /**
2760    * Creates and shows a new view of the current alignment.
2761    *
2762    * @param viewTitle
2763    *          title of newly created view; if null, one will be generated
2764    * @param copyAnnotation
2765    *          if true then duplicate all annnotation, groups and settings
2766    * @return new alignment panel, already displayed.
2767    */
2768   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2769   {
2770     /*
2771      * Create a new AlignmentPanel (with its own, new Viewport)
2772      */
2773     AlignmentPanel newap = new jalview.project.Jalview2XML()
2774             .copyAlignPanel(alignPanel);
2775     if (!copyAnnotation)
2776     {
2777       /*
2778        * remove all groups and annotation except for the automatic stuff
2779        */
2780       newap.av.getAlignment().deleteAllGroups();
2781       newap.av.getAlignment().deleteAllAnnotations(false);
2782     }
2783
2784     newap.av.setGatherViewsHere(false);
2785
2786     if (viewport.getViewName() == null)
2787     {
2788       viewport.setViewName(MessageManager
2789               .getString("label.view_name_original"));
2790     }
2791
2792     /*
2793      * Views share the same edits undo and redo stacks
2794      */
2795     newap.av.setHistoryList(viewport.getHistoryList());
2796     newap.av.setRedoList(viewport.getRedoList());
2797
2798     /*
2799      * Views share the same mappings; need to deregister any new mappings
2800      * created by copyAlignPanel, and register the new reference to the shared
2801      * mappings
2802      */
2803     newap.av.replaceMappings(viewport.getAlignment());
2804
2805     /*
2806      * start up cDNA consensus (if applicable) now mappings are in place
2807      */
2808     if (newap.av.initComplementConsensus())
2809     {
2810       newap.refresh(true); // adjust layout of annotations
2811     }
2812
2813     newap.av.setViewName(getNewViewName(viewTitle));
2814
2815     addAlignmentPanel(newap, true);
2816     newap.alignmentChanged();
2817
2818     if (alignPanels.size() == 2)
2819     {
2820       viewport.setGatherViewsHere(true);
2821     }
2822     tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2823     return newap;
2824   }
2825
2826   /**
2827    * Make a new name for the view, ensuring it is unique within the current
2828    * sequenceSetId. (This used to be essential for Jalview Project archives, but
2829    * these now use viewId. Unique view names are still desirable for usability.)
2830    *
2831    * @param viewTitle
2832    * @return
2833    */
2834   protected String getNewViewName(String viewTitle)
2835   {
2836     int index = Desktop.getViewCount(viewport.getSequenceSetId());
2837     boolean addFirstIndex = false;
2838     if (viewTitle == null || viewTitle.trim().length() == 0)
2839     {
2840       viewTitle = MessageManager.getString("action.view");
2841       addFirstIndex = true;
2842     }
2843     else
2844     {
2845       index = 1;// we count from 1 if given a specific name
2846     }
2847     String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2848
2849     List<Component> comps = PaintRefresher.components
2850             .get(viewport.getSequenceSetId());
2851
2852     List<String> existingNames = getExistingViewNames(comps);
2853
2854     while (existingNames.contains(newViewName))
2855     {
2856       newViewName = viewTitle + " " + (++index);
2857     }
2858     return newViewName;
2859   }
2860
2861   /**
2862    * Returns a list of distinct view names found in the given list of
2863    * components. View names are held on the viewport of an AlignmentPanel.
2864    *
2865    * @param comps
2866    * @return
2867    */
2868   protected List<String> getExistingViewNames(List<Component> comps)
2869   {
2870     List<String> existingNames = new ArrayList<>();
2871     for (Component comp : comps)
2872     {
2873       if (comp instanceof AlignmentPanel)
2874       {
2875         AlignmentPanel ap = (AlignmentPanel) comp;
2876         if (!existingNames.contains(ap.av.getViewName()))
2877         {
2878           existingNames.add(ap.av.getViewName());
2879         }
2880       }
2881     }
2882     return existingNames;
2883   }
2884
2885   /**
2886    * Explode tabbed views into separate windows.
2887    */
2888   @Override
2889   public void expandViews_actionPerformed(ActionEvent e)
2890   {
2891     Desktop.explodeViews(this);
2892   }
2893
2894   /**
2895    * Gather views in separate windows back into a tabbed presentation.
2896    */
2897   @Override
2898   public void gatherViews_actionPerformed(ActionEvent e)
2899   {
2900     Desktop.instance.gatherViews(this);
2901   }
2902
2903   /**
2904    * DOCUMENT ME!
2905    *
2906    * @param e
2907    *          DOCUMENT ME!
2908    */
2909   @Override
2910   public void font_actionPerformed(ActionEvent e)
2911   {
2912     new FontChooser(alignPanel);
2913   }
2914
2915   /**
2916    * DOCUMENT ME!
2917    *
2918    * @param e
2919    *          DOCUMENT ME!
2920    */
2921   @Override
2922   protected void seqLimit_actionPerformed(ActionEvent e)
2923   {
2924     viewport.setShowJVSuffix(seqLimits.isSelected());
2925
2926     alignPanel.getIdPanel().getIdCanvas()
2927             .setPreferredSize(alignPanel.calculateIdWidth());
2928     alignPanel.paintAlignment(true, false);
2929   }
2930
2931   @Override
2932   public void idRightAlign_actionPerformed(ActionEvent e)
2933   {
2934     viewport.setRightAlignIds(idRightAlign.isSelected());
2935     alignPanel.paintAlignment(false, false);
2936   }
2937
2938   @Override
2939   public void centreColumnLabels_actionPerformed(ActionEvent e)
2940   {
2941     viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2942     alignPanel.paintAlignment(false, false);
2943   }
2944
2945   /*
2946    * (non-Javadoc)
2947    *
2948    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2949    */
2950   @Override
2951   protected void followHighlight_actionPerformed()
2952   {
2953     /*
2954      * Set the 'follow' flag on the Viewport (and scroll to position if now
2955      * true).
2956      */
2957     final boolean state = this.followHighlightMenuItem.getState();
2958     viewport.setFollowHighlight(state);
2959     if (state)
2960     {
2961       alignPanel.scrollToPosition(viewport.getSearchResults(), false);
2962     }
2963   }
2964
2965   /**
2966    * DOCUMENT ME!
2967    *
2968    * @param e
2969    *          DOCUMENT ME!
2970    */
2971   @Override
2972   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2973   {
2974     viewport.setColourText(colourTextMenuItem.isSelected());
2975     alignPanel.paintAlignment(false, false);
2976   }
2977
2978   /**
2979    * DOCUMENT ME!
2980    *
2981    * @param e
2982    *          DOCUMENT ME!
2983    */
2984   @Override
2985   public void wrapMenuItem_actionPerformed(ActionEvent e)
2986   {
2987     scaleAbove.setVisible(wrapMenuItem.isSelected());
2988     scaleLeft.setVisible(wrapMenuItem.isSelected());
2989     scaleRight.setVisible(wrapMenuItem.isSelected());
2990     viewport.setWrapAlignment(wrapMenuItem.isSelected());
2991     alignPanel.updateLayout();
2992   }
2993
2994   @Override
2995   public void showAllSeqs_actionPerformed(ActionEvent e)
2996   {
2997     viewport.showAllHiddenSeqs();
2998   }
2999
3000   @Override
3001   public void showAllColumns_actionPerformed(ActionEvent e)
3002   {
3003     viewport.showAllHiddenColumns();
3004     alignPanel.paintAlignment(true, true);
3005     viewport.sendSelection();
3006   }
3007
3008   @Override
3009   public void hideSelSequences_actionPerformed(ActionEvent e)
3010   {
3011     viewport.hideAllSelectedSeqs();
3012   }
3013
3014   /**
3015    * called by key handler and the hide all/show all menu items
3016    *
3017    * @param toggleSeqs
3018    * @param toggleCols
3019    */
3020   private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3021   {
3022
3023     boolean hide = false;
3024     SequenceGroup sg = viewport.getSelectionGroup();
3025     if (!toggleSeqs && !toggleCols)
3026     {
3027       // Hide everything by the current selection - this is a hack - we do the
3028       // invert and then hide
3029       // first check that there will be visible columns after the invert.
3030       if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3031               && sg.getStartRes() <= sg.getEndRes()))
3032       {
3033         // now invert the sequence set, if required - empty selection implies
3034         // that no hiding is required.
3035         if (sg != null)
3036         {
3037           invertSequenceMenuItem_actionPerformed(null);
3038           sg = viewport.getSelectionGroup();
3039           toggleSeqs = true;
3040
3041         }
3042         viewport.expandColSelection(sg, true);
3043         // finally invert the column selection and get the new sequence
3044         // selection.
3045         invertColSel_actionPerformed(null);
3046         toggleCols = true;
3047       }
3048     }
3049
3050     if (toggleSeqs)
3051     {
3052       if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3053       {
3054         hideSelSequences_actionPerformed(null);
3055         hide = true;
3056       }
3057       else if (!(toggleCols && viewport.hasSelectedColumns()))
3058       {
3059         showAllSeqs_actionPerformed(null);
3060       }
3061     }
3062
3063     if (toggleCols)
3064     {
3065       if (viewport.hasSelectedColumns())
3066       {
3067         hideSelColumns_actionPerformed(null);
3068         if (!toggleSeqs)
3069         {
3070           viewport.setSelectionGroup(sg);
3071         }
3072       }
3073       else if (!hide)
3074       {
3075         showAllColumns_actionPerformed(null);
3076       }
3077     }
3078   }
3079
3080   /*
3081    * (non-Javadoc)
3082    *
3083    * @see
3084    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3085    * event.ActionEvent)
3086    */
3087   @Override
3088   public void hideAllButSelection_actionPerformed(ActionEvent e)
3089   {
3090     toggleHiddenRegions(false, false);
3091     viewport.sendSelection();
3092   }
3093
3094   /*
3095    * (non-Javadoc)
3096    *
3097    * @see
3098    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3099    * .ActionEvent)
3100    */
3101   @Override
3102   public void hideAllSelection_actionPerformed(ActionEvent e)
3103   {
3104     SequenceGroup sg = viewport.getSelectionGroup();
3105     viewport.expandColSelection(sg, false);
3106     viewport.hideAllSelectedSeqs();
3107     viewport.hideSelectedColumns();
3108     alignPanel.paintAlignment(true, true);
3109     viewport.sendSelection();
3110   }
3111
3112   /*
3113    * (non-Javadoc)
3114    *
3115    * @see
3116    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3117    * ActionEvent)
3118    */
3119   @Override
3120   public void showAllhidden_actionPerformed(ActionEvent e)
3121   {
3122     viewport.showAllHiddenColumns();
3123     viewport.showAllHiddenSeqs();
3124     alignPanel.paintAlignment(true, true);
3125     viewport.sendSelection();
3126   }
3127
3128   @Override
3129   public void hideSelColumns_actionPerformed(ActionEvent e)
3130   {
3131     viewport.hideSelectedColumns();
3132     alignPanel.paintAlignment(true, true);
3133     viewport.sendSelection();
3134   }
3135
3136   @Override
3137   public void hiddenMarkers_actionPerformed(ActionEvent e)
3138   {
3139     viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3140     repaint();
3141   }
3142
3143   /**
3144    * DOCUMENT ME!
3145    *
3146    * @param e
3147    *          DOCUMENT ME!
3148    */
3149   @Override
3150   protected void scaleAbove_actionPerformed(ActionEvent e)
3151   {
3152     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3153     // TODO: do we actually need to update overview for scale above change ?
3154     alignPanel.paintAlignment(true, false);
3155   }
3156
3157   /**
3158    * DOCUMENT ME!
3159    *
3160    * @param e
3161    *          DOCUMENT ME!
3162    */
3163   @Override
3164   protected void scaleLeft_actionPerformed(ActionEvent e)
3165   {
3166     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3167     alignPanel.paintAlignment(true, false);
3168   }
3169
3170   /**
3171    * DOCUMENT ME!
3172    *
3173    * @param e
3174    *          DOCUMENT ME!
3175    */
3176   @Override
3177   protected void scaleRight_actionPerformed(ActionEvent e)
3178   {
3179     viewport.setScaleRightWrapped(scaleRight.isSelected());
3180     alignPanel.paintAlignment(true, false);
3181   }
3182
3183   /**
3184    * DOCUMENT ME!
3185    *
3186    * @param e
3187    *          DOCUMENT ME!
3188    */
3189   @Override
3190   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3191   {
3192     viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3193     alignPanel.paintAlignment(false, false);
3194   }
3195
3196   /**
3197    * DOCUMENT ME!
3198    *
3199    * @param e
3200    *          DOCUMENT ME!
3201    */
3202   @Override
3203   public void viewTextMenuItem_actionPerformed(ActionEvent e)
3204   {
3205     viewport.setShowText(viewTextMenuItem.isSelected());
3206     alignPanel.paintAlignment(false, false);
3207   }
3208
3209   /**
3210    * DOCUMENT ME!
3211    *
3212    * @param e
3213    *          DOCUMENT ME!
3214    */
3215   @Override
3216   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3217   {
3218     viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3219     alignPanel.paintAlignment(false, false);
3220   }
3221
3222   public FeatureSettings featureSettings;
3223
3224   @Override
3225   public FeatureSettingsControllerI getFeatureSettingsUI()
3226   {
3227     return featureSettings;
3228   }
3229
3230   @Override
3231   public void featureSettings_actionPerformed(ActionEvent e)
3232   {
3233     if (featureSettings != null)
3234     {
3235       featureSettings.close();
3236       featureSettings = null;
3237     }
3238     if (!showSeqFeatures.isSelected())
3239     {
3240       // make sure features are actually displayed
3241       showSeqFeatures.setSelected(true);
3242       showSeqFeatures_actionPerformed(null);
3243     }
3244     featureSettings = new FeatureSettings(this);
3245   }
3246
3247   /**
3248    * Set or clear 'Show Sequence Features'
3249    *
3250    * @param evt
3251    *          DOCUMENT ME!
3252    */
3253   @Override
3254   public void showSeqFeatures_actionPerformed(ActionEvent evt)
3255   {
3256     viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3257     alignPanel.paintAlignment(true, true);
3258   }
3259
3260   /**
3261    * Action on toggle of the 'Show annotations' menu item. This shows or hides
3262    * the annotations panel as a whole.
3263    *
3264    * The options to show/hide all annotations should be enabled when the panel
3265    * is shown, and disabled when the panel is hidden.
3266    *
3267    * @param e
3268    */
3269   @Override
3270   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3271   {
3272     final boolean setVisible = annotationPanelMenuItem.isSelected();
3273     viewport.setShowAnnotation(setVisible);
3274     this.showAllSeqAnnotations.setEnabled(setVisible);
3275     this.hideAllSeqAnnotations.setEnabled(setVisible);
3276     this.showAllAlAnnotations.setEnabled(setVisible);
3277     this.hideAllAlAnnotations.setEnabled(setVisible);
3278     alignPanel.updateLayout();
3279   }
3280
3281   @Override
3282   public void alignmentProperties()
3283   {
3284     JComponent pane;
3285     StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3286
3287             .formatAsHtml();
3288     String content = MessageManager.formatMessage("label.html_content",
3289             new Object[]
3290             { contents.toString() });
3291     contents = null;
3292
3293     if (Platform.isJS())
3294     {
3295       JLabel textLabel = new JLabel();
3296       textLabel.setText(content);
3297       textLabel.setBackground(Color.WHITE);
3298
3299       pane = new JPanel(new BorderLayout());
3300       ((JPanel) pane).setOpaque(true);
3301       pane.setBackground(Color.WHITE);
3302       ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3303     }
3304     else
3305     {
3306       JEditorPane editPane = new JEditorPane("text/html", "");
3307       editPane.setEditable(false);
3308       editPane.setText(content);
3309       pane = editPane;
3310     }
3311
3312     JInternalFrame frame = new JInternalFrame();
3313
3314     frame.getContentPane().add(new JScrollPane(pane));
3315
3316     Desktop.addInternalFrame(frame, MessageManager
3317             .formatMessage("label.alignment_properties", new Object[]
3318             { getTitle() }), 500, 400);
3319   }
3320
3321   /**
3322    * DOCUMENT ME!
3323    *
3324    * @param e
3325    *          DOCUMENT ME!
3326    */
3327   @Override
3328   public void overviewMenuItem_actionPerformed(ActionEvent e)
3329   {
3330     if (alignPanel.overviewPanel != null)
3331     {
3332       return;
3333     }
3334
3335     JInternalFrame frame = new JInternalFrame();
3336     final OverviewPanel overview = new OverviewPanel(alignPanel);
3337     frame.setContentPane(overview);
3338     Desktop.addInternalFrame(frame, MessageManager
3339             .formatMessage("label.overview_params", new Object[]
3340             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3341             true, true);
3342     frame.pack();
3343     frame.setLayer(JLayeredPane.PALETTE_LAYER);
3344     frame.addInternalFrameListener(
3345             new javax.swing.event.InternalFrameAdapter()
3346             {
3347               @Override
3348               public void internalFrameClosed(
3349                       javax.swing.event.InternalFrameEvent evt)
3350               {
3351                 overview.dispose();
3352                 alignPanel.setOverviewPanel(null);
3353               };
3354             });
3355     if (getKeyListeners().length > 0)
3356     {
3357       frame.addKeyListener(getKeyListeners()[0]);
3358     }
3359
3360     alignPanel.setOverviewPanel(overview);
3361   }
3362
3363   @Override
3364   public void textColour_actionPerformed()
3365   {
3366     new TextColourChooser().chooseColour(alignPanel, null);
3367   }
3368
3369   /*
3370    * public void covariationColour_actionPerformed() {
3371    * changeColour(new
3372    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3373    * ()[0])); }
3374    */
3375   @Override
3376   public void annotationColour_actionPerformed()
3377   {
3378     new AnnotationColourChooser(viewport, alignPanel);
3379   }
3380
3381   @Override
3382   public void annotationColumn_actionPerformed(ActionEvent e)
3383   {
3384     new AnnotationColumnChooser(viewport, alignPanel);
3385   }
3386
3387   /**
3388    * Action on the user checking or unchecking the option to apply the selected
3389    * colour scheme to all groups. If unchecked, groups may have their own
3390    * independent colour schemes.
3391    *
3392    * @param selected
3393    */
3394   @Override
3395   public void applyToAllGroups_actionPerformed(boolean selected)
3396   {
3397     viewport.setColourAppliesToAllGroups(selected);
3398   }
3399
3400   /**
3401    * Action on user selecting a colour from the colour menu
3402    *
3403    * @param name
3404    *          the name (not the menu item label!) of the colour scheme
3405    */
3406   @Override
3407   public void changeColour_actionPerformed(String name)
3408   {
3409     /*
3410      * 'User Defined' opens a panel to configure or load a
3411      * user-defined colour scheme
3412      */
3413     if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3414     {
3415       new UserDefinedColours(alignPanel);
3416       return;
3417     }
3418
3419     /*
3420      * otherwise set the chosen colour scheme (or null for 'None')
3421      */
3422     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3423             viewport.getAlignment(), viewport.getHiddenRepSequences());
3424     changeColour(cs);
3425   }
3426
3427   /**
3428    * Actions on setting or changing the alignment colour scheme
3429    *
3430    * @param cs
3431    */
3432   @Override
3433   public void changeColour(ColourSchemeI cs)
3434   {
3435     // TODO: pull up to controller method
3436     ColourMenuHelper.setColourSelected(colourMenu, cs);
3437
3438     viewport.setGlobalColourScheme(cs);
3439
3440     alignPanel.paintAlignment(true, true);
3441   }
3442
3443   /**
3444    * Show the PID threshold slider panel
3445    */
3446   @Override
3447   protected void modifyPID_actionPerformed()
3448   {
3449     SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3450             alignPanel.getViewName());
3451     SliderPanel.showPIDSlider();
3452   }
3453
3454   /**
3455    * Show the Conservation slider panel
3456    */
3457   @Override
3458   protected void modifyConservation_actionPerformed()
3459   {
3460     SliderPanel.setConservationSlider(alignPanel,
3461             viewport.getResidueShading(), alignPanel.getViewName());
3462     SliderPanel.showConservationSlider();
3463   }
3464
3465   /**
3466    * Action on selecting or deselecting (Colour) By Conservation
3467    */
3468   @Override
3469   public void conservationMenuItem_actionPerformed(boolean selected)
3470   {
3471     modifyConservation.setEnabled(selected);
3472     viewport.setConservationSelected(selected);
3473     viewport.getResidueShading().setConservationApplied(selected);
3474
3475     changeColour(viewport.getGlobalColourScheme());
3476     if (selected)
3477     {
3478       modifyConservation_actionPerformed();
3479     }
3480     else
3481     {
3482       SliderPanel.hideConservationSlider();
3483     }
3484   }
3485
3486   /**
3487    * Action on selecting or deselecting (Colour) Above PID Threshold
3488    */
3489   @Override
3490   public void abovePIDThreshold_actionPerformed(boolean selected)
3491   {
3492     modifyPID.setEnabled(selected);
3493     viewport.setAbovePIDThreshold(selected);
3494     if (!selected)
3495     {
3496       viewport.getResidueShading().setThreshold(0,
3497               viewport.isIgnoreGapsConsensus());
3498     }
3499
3500     changeColour(viewport.getGlobalColourScheme());
3501     if (selected)
3502     {
3503       modifyPID_actionPerformed();
3504     }
3505     else
3506     {
3507       SliderPanel.hidePIDSlider();
3508     }
3509   }
3510
3511   /**
3512    * DOCUMENT ME!
3513    *
3514    * @param e
3515    *          DOCUMENT ME!
3516    */
3517   @Override
3518   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3519   {
3520     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3521     AlignmentSorter.sortByPID(viewport.getAlignment(),
3522             viewport.getAlignment().getSequenceAt(0));
3523     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3524             viewport.getAlignment()));
3525     alignPanel.paintAlignment(true, false);
3526   }
3527
3528   /**
3529    * DOCUMENT ME!
3530    *
3531    * @param e
3532    *          DOCUMENT ME!
3533    */
3534   @Override
3535   public void sortIDMenuItem_actionPerformed(ActionEvent e)
3536   {
3537     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3538     AlignmentSorter.sortByID(viewport.getAlignment());
3539     addHistoryItem(
3540             new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3541     alignPanel.paintAlignment(true, false);
3542   }
3543
3544   /**
3545    * DOCUMENT ME!
3546    *
3547    * @param e
3548    *          DOCUMENT ME!
3549    */
3550   @Override
3551   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3552   {
3553     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3554     AlignmentSorter.sortByLength(viewport.getAlignment());
3555     addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3556             viewport.getAlignment()));
3557     alignPanel.paintAlignment(true, false);
3558   }
3559
3560   /**
3561    * DOCUMENT ME!
3562    *
3563    * @param e
3564    *          DOCUMENT ME!
3565    */
3566   @Override
3567   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3568   {
3569     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3570     AlignmentSorter.sortByGroup(viewport.getAlignment());
3571     addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3572             viewport.getAlignment()));
3573
3574     alignPanel.paintAlignment(true, false);
3575   }
3576
3577   /**
3578    * DOCUMENT ME!
3579    *
3580    * @param e
3581    *          DOCUMENT ME!
3582    */
3583   @Override
3584   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3585   {
3586     new RedundancyPanel(alignPanel, this);
3587   }
3588
3589   /**
3590    * DOCUMENT ME!
3591    *
3592    * @param e
3593    *          DOCUMENT ME!
3594    */
3595   @Override
3596   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3597   {
3598     if ((viewport.getSelectionGroup() == null)
3599             || (viewport.getSelectionGroup().getSize() < 2))
3600     {
3601       JvOptionPane.showInternalMessageDialog(this,
3602               MessageManager.getString(
3603                       "label.you_must_select_least_two_sequences"),
3604               MessageManager.getString("label.invalid_selection"),
3605               JvOptionPane.WARNING_MESSAGE);
3606     }
3607     else
3608     {
3609       JInternalFrame frame = new JInternalFrame();
3610       frame.setContentPane(new PairwiseAlignPanel(viewport));
3611       Desktop.addInternalFrame(frame,
3612               MessageManager.getString("action.pairwise_alignment"), 600,
3613               500);
3614     }
3615   }
3616
3617   @Override
3618   public void autoCalculate_actionPerformed(ActionEvent e)
3619   {
3620     viewport.autoCalculateConsensus = autoCalculate.isSelected();
3621     if (viewport.autoCalculateConsensus)
3622     {
3623       viewport.firePropertyChange("alignment", null,
3624               viewport.getAlignment().getSequences());
3625     }
3626   }
3627
3628   @Override
3629   public void sortByTreeOption_actionPerformed(ActionEvent e)
3630   {
3631     viewport.sortByTree = sortByTree.isSelected();
3632   }
3633
3634   @Override
3635   protected void listenToViewSelections_actionPerformed(ActionEvent e)
3636   {
3637     viewport.followSelection = listenToViewSelections.isSelected();
3638   }
3639
3640   /**
3641    * Constructs a tree panel and adds it to the desktop
3642    *
3643    * @param type
3644    *          tree type (NJ or AV)
3645    * @param modelName
3646    *          name of score model used to compute the tree
3647    * @param options
3648    *          parameters for the distance or similarity calculation
3649    */
3650   void newTreePanel(String type, String modelName,
3651           SimilarityParamsI options)
3652   {
3653     String frameTitle = "";
3654     TreePanel tp;
3655
3656     boolean onSelection = false;
3657     if (viewport.getSelectionGroup() != null
3658             && viewport.getSelectionGroup().getSize() > 0)
3659     {
3660       SequenceGroup sg = viewport.getSelectionGroup();
3661
3662       /* Decide if the selection is a column region */
3663       for (SequenceI _s : sg.getSequences())
3664       {
3665         if (_s.getLength() < sg.getEndRes())
3666         {
3667           JvOptionPane.showMessageDialog(Desktop.desktop,
3668                   MessageManager.getString(
3669                           "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3670                   MessageManager.getString(
3671                           "label.sequences_selection_not_aligned"),
3672                   JvOptionPane.WARNING_MESSAGE);
3673
3674           return;
3675         }
3676       }
3677       onSelection = true;
3678     }
3679     else
3680     {
3681       if (viewport.getAlignment().getHeight() < 2)
3682       {
3683         return;
3684       }
3685     }
3686
3687     tp = new TreePanel(alignPanel, type, modelName, options);
3688     frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3689
3690     frameTitle += " from ";
3691
3692     if (viewport.getViewName() != null)
3693     {
3694       frameTitle += viewport.getViewName() + " of ";
3695     }
3696
3697     frameTitle += this.title;
3698
3699     Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3700   }
3701
3702   /**
3703    * DOCUMENT ME!
3704    *
3705    * @param title
3706    *          DOCUMENT ME!
3707    * @param order
3708    *          DOCUMENT ME!
3709    */
3710   public void addSortByOrderMenuItem(String title,
3711           final AlignmentOrder order)
3712   {
3713     final JMenuItem item = new JMenuItem(MessageManager
3714             .formatMessage("action.by_title_param", new Object[]
3715             { title }));
3716     sort.add(item);
3717     item.addActionListener(new java.awt.event.ActionListener()
3718     {
3719       @Override
3720       public void actionPerformed(ActionEvent e)
3721       {
3722         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3723
3724         // TODO: JBPNote - have to map order entries to curent SequenceI
3725         // pointers
3726         AlignmentSorter.sortBy(viewport.getAlignment(), order);
3727
3728         addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3729                 viewport.getAlignment()));
3730
3731         alignPanel.paintAlignment(true, false);
3732       }
3733     });
3734   }
3735
3736   /**
3737    * Add a new sort by annotation score menu item
3738    *
3739    * @param sort
3740    *          the menu to add the option to
3741    * @param scoreLabel
3742    *          the label used to retrieve scores for each sequence on the
3743    *          alignment
3744    */
3745   public void addSortByAnnotScoreMenuItem(JMenu sort,
3746           final String scoreLabel)
3747   {
3748     final JMenuItem item = new JMenuItem(scoreLabel);
3749     sort.add(item);
3750     item.addActionListener(new java.awt.event.ActionListener()
3751     {
3752       @Override
3753       public void actionPerformed(ActionEvent e)
3754       {
3755         SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3756         AlignmentSorter.sortByAnnotationScore(scoreLabel,
3757                 viewport.getAlignment());// ,viewport.getSelectionGroup());
3758         addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3759                 viewport.getAlignment()));
3760         alignPanel.paintAlignment(true, false);
3761       }
3762     });
3763   }
3764
3765   /**
3766    * last hash for alignment's annotation array - used to minimise cost of
3767    * rebuild.
3768    */
3769   protected int _annotationScoreVectorHash;
3770
3771   /**
3772    * search the alignment and rebuild the sort by annotation score submenu the
3773    * last alignment annotation vector hash is stored to minimize cost of
3774    * rebuilding in subsequence calls.
3775    *
3776    */
3777   @Override
3778   public void buildSortByAnnotationScoresMenu()
3779   {
3780     if (viewport.getAlignment().getAlignmentAnnotation() == null)
3781     {
3782       return;
3783     }
3784
3785     if (viewport.getAlignment().getAlignmentAnnotation()
3786             .hashCode() != _annotationScoreVectorHash)
3787     {
3788       sortByAnnotScore.removeAll();
3789       // almost certainly a quicker way to do this - but we keep it simple
3790       Hashtable scoreSorts = new Hashtable();
3791       AlignmentAnnotation aann[];
3792       for (SequenceI sqa : viewport.getAlignment().getSequences())
3793       {
3794         aann = sqa.getAnnotation();
3795         for (int i = 0; aann != null && i < aann.length; i++)
3796         {
3797           if (aann[i].hasScore() && aann[i].sequenceRef != null)
3798           {
3799             scoreSorts.put(aann[i].label, aann[i].label);
3800           }
3801         }
3802       }
3803       Enumeration labels = scoreSorts.keys();
3804       while (labels.hasMoreElements())
3805       {
3806         addSortByAnnotScoreMenuItem(sortByAnnotScore,
3807                 (String) labels.nextElement());
3808       }
3809       sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3810       scoreSorts.clear();
3811
3812       _annotationScoreVectorHash = viewport.getAlignment()
3813               .getAlignmentAnnotation().hashCode();
3814     }
3815   }
3816
3817   /**
3818    * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3819    * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3820    * call. Listeners are added to remove the menu item when the treePanel is
3821    * closed, and adjust the tree leaf to sequence mapping when the alignment is
3822    * modified.
3823    */
3824   @Override
3825   public void buildTreeSortMenu()
3826   {
3827     sortByTreeMenu.removeAll();
3828
3829     List<Component> comps = PaintRefresher.components
3830             .get(viewport.getSequenceSetId());
3831     List<TreePanel> treePanels = new ArrayList<>();
3832     for (Component comp : comps)
3833     {
3834       if (comp instanceof TreePanel)
3835       {
3836         treePanels.add((TreePanel) comp);
3837       }
3838     }
3839
3840     if (treePanels.size() < 1)
3841     {
3842       sortByTreeMenu.setVisible(false);
3843       return;
3844     }
3845
3846     sortByTreeMenu.setVisible(true);
3847
3848     for (final TreePanel tp : treePanels)
3849     {
3850       final JMenuItem item = new JMenuItem(tp.getTitle());
3851       item.addActionListener(new java.awt.event.ActionListener()
3852       {
3853         @Override
3854         public void actionPerformed(ActionEvent e)
3855         {
3856           tp.sortByTree_actionPerformed();
3857           addHistoryItem(tp.sortAlignmentIn(alignPanel));
3858
3859         }
3860       });
3861
3862       sortByTreeMenu.add(item);
3863     }
3864   }
3865
3866   public boolean sortBy(AlignmentOrder alorder, String undoname)
3867   {
3868     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3869     AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3870     if (undoname != null)
3871     {
3872       addHistoryItem(new OrderCommand(undoname, oldOrder,
3873               viewport.getAlignment()));
3874     }
3875     alignPanel.paintAlignment(true, false);
3876     return true;
3877   }
3878
3879   /**
3880    * Work out whether the whole set of sequences or just the selected set will
3881    * be submitted for multiple alignment.
3882    *
3883    */
3884   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3885   {
3886     // Now, check we have enough sequences
3887     AlignmentView msa = null;
3888
3889     if ((viewport.getSelectionGroup() != null)
3890             && (viewport.getSelectionGroup().getSize() > 1))
3891     {
3892       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3893       // some common interface!
3894       /*
3895        * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3896        * SequenceI[sz = seqs.getSize(false)];
3897        *
3898        * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3899        * seqs.getSequenceAt(i); }
3900        */
3901       msa = viewport.getAlignmentView(true);
3902     }
3903     else if (viewport.getSelectionGroup() != null
3904             && viewport.getSelectionGroup().getSize() == 1)
3905     {
3906       int option = JvOptionPane.showConfirmDialog(this,
3907               MessageManager.getString("warn.oneseq_msainput_selection"),
3908               MessageManager.getString("label.invalid_selection"),
3909               JvOptionPane.OK_CANCEL_OPTION);
3910       if (option == JvOptionPane.OK_OPTION)
3911       {
3912         msa = viewport.getAlignmentView(false);
3913       }
3914     }
3915     else
3916     {
3917       msa = viewport.getAlignmentView(false);
3918     }
3919     return msa;
3920   }
3921
3922   /**
3923    * Decides what is submitted to a secondary structure prediction service: the
3924    * first sequence in the alignment, or in the current selection, or, if the
3925    * alignment is 'aligned' (ie padded with gaps), then the currently selected
3926    * region or the whole alignment. (where the first sequence in the set is the
3927    * one that the prediction will be for).
3928    */
3929   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3930   {
3931     AlignmentView seqs = null;
3932
3933     if ((viewport.getSelectionGroup() != null)
3934             && (viewport.getSelectionGroup().getSize() > 0))
3935     {
3936       seqs = viewport.getAlignmentView(true);
3937     }
3938     else
3939     {
3940       seqs = viewport.getAlignmentView(false);
3941     }
3942     // limit sequences - JBPNote in future - could spawn multiple prediction
3943     // jobs
3944     // TODO: viewport.getAlignment().isAligned is a global state - the local
3945     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3946     if (!viewport.getAlignment().isAligned(false))
3947     {
3948       seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3949       // TODO: if seqs.getSequences().length>1 then should really have warned
3950       // user!
3951
3952     }
3953     return seqs;
3954   }
3955
3956   /**
3957    * DOCUMENT ME!
3958    *
3959    * @param e
3960    *          DOCUMENT ME!
3961    */
3962   @Override
3963   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3964   {
3965     // Pick the tree file
3966     JalviewFileChooser chooser = new JalviewFileChooser(
3967             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3968     chooser.setFileView(new JalviewFileView());
3969     chooser.setDialogTitle(
3970             MessageManager.getString("label.select_newick_like_tree_file"));
3971     chooser.setToolTipText(
3972             MessageManager.getString("label.load_tree_file"));
3973
3974     chooser.setResponseHandler(0,new Runnable()
3975     {
3976       @Override
3977       public void run()
3978       {
3979         String filePath = chooser.getSelectedFile().getPath();
3980         Cache.setProperty("LAST_DIRECTORY", filePath);
3981         NewickFile fin = null;
3982         try
3983         {
3984           fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
3985                   DataSourceType.FILE));
3986           viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
3987         } catch (Exception ex)
3988         {
3989           JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
3990                   MessageManager
3991                           .getString("label.problem_reading_tree_file"),
3992                   JvOptionPane.WARNING_MESSAGE);
3993           ex.printStackTrace();
3994         }
3995         if (fin != null && fin.hasWarningMessage())
3996         {
3997           JvOptionPane.showMessageDialog(Desktop.desktop,
3998                   fin.getWarningMessage(),
3999                   MessageManager.getString(
4000                           "label.possible_problem_with_tree_file"),
4001                   JvOptionPane.WARNING_MESSAGE);
4002         }
4003       }
4004     });
4005     chooser.showOpenDialog(this);
4006   }
4007
4008   public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4009   {
4010     return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4011   }
4012
4013   public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4014           int h, int x, int y)
4015   {
4016     return showNewickTree(nf, treeTitle, null, w, h, x, y);
4017   }
4018
4019   /**
4020    * Add a treeviewer for the tree extracted from a Newick file object to the
4021    * current alignment view
4022    *
4023    * @param nf
4024    *          the tree
4025    * @param title
4026    *          tree viewer title
4027    * @param input
4028    *          Associated alignment input data (or null)
4029    * @param w
4030    *          width
4031    * @param h
4032    *          height
4033    * @param x
4034    *          position
4035    * @param y
4036    *          position
4037    * @return TreePanel handle
4038    */
4039   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4040           AlignmentView input, int w, int h, int x, int y)
4041   {
4042     TreePanel tp = null;
4043
4044     try
4045     {
4046       nf.parse();
4047
4048       if (nf.getTree() != null)
4049       {
4050         tp = new TreePanel(alignPanel, nf, treeTitle, input);
4051
4052         tp.setSize(w, h);
4053
4054         if (x > 0 && y > 0)
4055         {
4056           tp.setLocation(x, y);
4057         }
4058
4059         Desktop.addInternalFrame(tp, treeTitle, w, h);
4060       }
4061     } catch (Exception ex)
4062     {
4063       ex.printStackTrace();
4064     }
4065
4066     return tp;
4067   }
4068
4069   private boolean buildingMenu = false;
4070
4071   /**
4072    * Generates menu items and listener event actions for web service clients
4073    *
4074    */
4075   public void BuildWebServiceMenu()
4076   {
4077     while (buildingMenu)
4078     {
4079       try
4080       {
4081         System.err.println("Waiting for building menu to finish.");
4082         Thread.sleep(10);
4083       } catch (Exception e)
4084       {
4085       }
4086     }
4087     final AlignFrame me = this;
4088     buildingMenu = true;
4089     new Thread(new Runnable()
4090     {
4091       @Override
4092       public void run()
4093       {
4094         final List<JMenuItem> legacyItems = new ArrayList<>();
4095         try
4096         {
4097           // System.err.println("Building ws menu again "
4098           // + Thread.currentThread());
4099           // TODO: add support for context dependent disabling of services based
4100           // on
4101           // alignment and current selection
4102           // TODO: add additional serviceHandle parameter to specify abstract
4103           // handler
4104           // class independently of AbstractName
4105           // TODO: add in rediscovery GUI function to restart discoverer
4106           // TODO: group services by location as well as function and/or
4107           // introduce
4108           // object broker mechanism.
4109           final Vector<JMenu> wsmenu = new Vector<>();
4110           final IProgressIndicator af = me;
4111
4112           /*
4113            * do not i18n these strings - they are hard-coded in class
4114            * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4115            * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4116            */
4117           final JMenu msawsmenu = new JMenu("Alignment");
4118           final JMenu secstrmenu = new JMenu(
4119                   "Secondary Structure Prediction");
4120           final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4121           final JMenu analymenu = new JMenu("Analysis");
4122           final JMenu dismenu = new JMenu("Protein Disorder");
4123           // JAL-940 - only show secondary structure prediction services from
4124           // the legacy server
4125           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4126               // &&
4127           Discoverer.services != null && (Discoverer.services.size() > 0))
4128           {
4129             // TODO: refactor to allow list of AbstractName/Handler bindings to
4130             // be
4131             // stored or retrieved from elsewhere
4132             // No MSAWS used any more:
4133             // Vector msaws = null; // (Vector)
4134             // Discoverer.services.get("MsaWS");
4135             Vector secstrpr = (Vector) Discoverer.services
4136                     .get("SecStrPred");
4137             if (secstrpr != null)
4138             {
4139               // Add any secondary structure prediction services
4140               for (int i = 0, j = secstrpr.size(); i < j; i++)
4141               {
4142                 final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
4143                         .get(i);
4144                 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4145                         .getServiceClient(sh);
4146                 int p = secstrmenu.getItemCount();
4147                 impl.attachWSMenuEntry(secstrmenu, me);
4148                 int q = secstrmenu.getItemCount();
4149                 for (int litm = p; litm < q; litm++)
4150                 {
4151                   legacyItems.add(secstrmenu.getItem(litm));
4152                 }
4153               }
4154             }
4155           }
4156
4157           // Add all submenus in the order they should appear on the web
4158           // services menu
4159           wsmenu.add(msawsmenu);
4160           wsmenu.add(secstrmenu);
4161           wsmenu.add(dismenu);
4162           wsmenu.add(analymenu);
4163           // No search services yet
4164           // wsmenu.add(seqsrchmenu);
4165
4166           javax.swing.SwingUtilities.invokeLater(new Runnable()
4167           {
4168             @Override
4169             public void run()
4170             {
4171               try
4172               {
4173                 webService.removeAll();
4174                 // first, add discovered services onto the webservices menu
4175                 if (wsmenu.size() > 0)
4176                 {
4177                   for (int i = 0, j = wsmenu.size(); i < j; i++)
4178                   {
4179                     webService.add(wsmenu.get(i));
4180                   }
4181                 }
4182                 else
4183                 {
4184                   webService.add(me.webServiceNoServices);
4185                 }
4186                 // TODO: move into separate menu builder class.
4187                 boolean new_sspred = false;
4188                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4189                 {
4190                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4191                   if (jws2servs != null)
4192                   {
4193                     if (jws2servs.hasServices())
4194                     {
4195                       jws2servs.attachWSMenuEntry(webService, me);
4196                       for (Jws2Instance sv : jws2servs.getServices())
4197                       {
4198                         if (sv.description.toLowerCase().contains("jpred"))
4199                         {
4200                           for (JMenuItem jmi : legacyItems)
4201                           {
4202                             jmi.setVisible(false);
4203                           }
4204                         }
4205                       }
4206
4207                     }
4208                     if (jws2servs.isRunning())
4209                     {
4210                       JMenuItem tm = new JMenuItem(
4211                               "Still discovering JABA Services");
4212                       tm.setEnabled(false);
4213                       webService.add(tm);
4214                     }
4215                   }
4216                 }
4217                 build_urlServiceMenu(me.webService);
4218                 build_fetchdbmenu(webService);
4219                 for (JMenu item : wsmenu)
4220                 {
4221                   if (item.getItemCount() == 0)
4222                   {
4223                     item.setEnabled(false);
4224                   }
4225                   else
4226                   {
4227                     item.setEnabled(true);
4228                   }
4229                 }
4230               } catch (Exception e)
4231               {
4232                 Cache.log.debug(
4233                         "Exception during web service menu building process.",
4234                         e);
4235               }
4236             }
4237           });
4238         } catch (Exception e)
4239         {
4240         }
4241         buildingMenu = false;
4242       }
4243     }).start();
4244
4245   }
4246
4247   /**
4248    * construct any groupURL type service menu entries.
4249    *
4250    * @param webService
4251    */
4252   private void build_urlServiceMenu(JMenu webService)
4253   {
4254     // TODO: remove this code when 2.7 is released
4255     // DEBUG - alignmentView
4256     /*
4257      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4258      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4259      *
4260      * @Override public void actionPerformed(ActionEvent e) {
4261      * jalview.datamodel.AlignmentView
4262      * .testSelectionViews(af.viewport.getAlignment(),
4263      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4264      *
4265      * }); webService.add(testAlView);
4266      */
4267     // TODO: refactor to RestClient discoverer and merge menu entries for
4268     // rest-style services with other types of analysis/calculation service
4269     // SHmmr test client - still being implemented.
4270     // DEBUG - alignmentView
4271
4272     for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4273             .getRestClients())
4274     {
4275       client.attachWSMenuEntry(
4276               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4277               this);
4278     }
4279   }
4280
4281   /**
4282    * Searches the alignment sequences for xRefs and builds the Show
4283    * Cross-References menu (formerly called Show Products), with database
4284    * sources for which cross-references are found (protein sources for a
4285    * nucleotide alignment and vice versa)
4286    *
4287    * @return true if Show Cross-references menu should be enabled
4288    */
4289   public boolean canShowProducts()
4290   {
4291     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4292     AlignmentI dataset = viewport.getAlignment().getDataset();
4293
4294     showProducts.removeAll();
4295     final boolean dna = viewport.getAlignment().isNucleotide();
4296
4297     if (seqs == null || seqs.length == 0)
4298     {
4299       // nothing to see here.
4300       return false;
4301     }
4302
4303     boolean showp = false;
4304     try
4305     {
4306       List<String> ptypes = new CrossRef(seqs, dataset)
4307               .findXrefSourcesForSequences(dna);
4308
4309       for (final String source : ptypes)
4310       {
4311         showp = true;
4312         final AlignFrame af = this;
4313         JMenuItem xtype = new JMenuItem(source);
4314         xtype.addActionListener(new ActionListener()
4315         {
4316           @Override
4317           public void actionPerformed(ActionEvent e)
4318           {
4319             showProductsFor(af.viewport.getSequenceSelection(), dna,
4320                     source);
4321           }
4322         });
4323         showProducts.add(xtype);
4324       }
4325       showProducts.setVisible(showp);
4326       showProducts.setEnabled(showp);
4327     } catch (Exception e)
4328     {
4329       Cache.log.warn(
4330               "canShowProducts threw an exception - please report to help@jalview.org",
4331               e);
4332       return false;
4333     }
4334     return showp;
4335   }
4336
4337   /**
4338    * Finds and displays cross-references for the selected sequences (protein
4339    * products for nucleotide sequences, dna coding sequences for peptides).
4340    *
4341    * @param sel
4342    *          the sequences to show cross-references for
4343    * @param dna
4344    *          true if from a nucleotide alignment (so showing proteins)
4345    * @param source
4346    *          the database to show cross-references for
4347    */
4348   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4349           final String source)
4350   {
4351     new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4352             .start();
4353   }
4354
4355   /**
4356    * Construct and display a new frame containing the translation of this
4357    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4358    */
4359   @Override
4360   public void showTranslation_actionPerformed(ActionEvent e)
4361   {
4362     AlignmentI al = null;
4363     try
4364     {
4365       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4366
4367       al = dna.translateCdna();
4368     } catch (Exception ex)
4369     {
4370       jalview.bin.Cache.log.error(
4371               "Exception during translation. Please report this !", ex);
4372       final String msg = MessageManager.getString(
4373               "label.error_when_translating_sequences_submit_bug_report");
4374       final String errorTitle = MessageManager
4375               .getString("label.implementation_error")
4376               + MessageManager.getString("label.translation_failed");
4377       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4378               JvOptionPane.ERROR_MESSAGE);
4379       return;
4380     }
4381     if (al == null || al.getHeight() == 0)
4382     {
4383       final String msg = MessageManager.getString(
4384               "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4385       final String errorTitle = MessageManager
4386               .getString("label.translation_failed");
4387       JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4388               JvOptionPane.WARNING_MESSAGE);
4389     }
4390     else
4391     {
4392       AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4393       af.setFileFormat(this.currentFileFormat);
4394       final String newTitle = MessageManager
4395               .formatMessage("label.translation_of_params", new Object[]
4396               { this.getTitle() });
4397       af.setTitle(newTitle);
4398       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4399       {
4400         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4401         viewport.openSplitFrame(af, new Alignment(seqs));
4402       }
4403       else
4404       {
4405         Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4406                 DEFAULT_HEIGHT);
4407       }
4408     }
4409   }
4410
4411   /**
4412    * Set the file format
4413    *
4414    * @param format
4415    */
4416   public void setFileFormat(FileFormatI format)
4417   {
4418     this.currentFileFormat = format;
4419   }
4420
4421   /**
4422    * Try to load a features file onto the alignment.
4423    *
4424    * @param file
4425    *          contents or path to retrieve file or a File object
4426    * @param sourceType
4427    *          access mode of file (see jalview.io.AlignFile)
4428    * @return true if features file was parsed correctly.
4429    */
4430   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4431   {
4432     // BH 2018
4433     return avc.parseFeaturesFile(file, sourceType,
4434             Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4435
4436   }
4437
4438   @Override
4439   public void refreshFeatureUI(boolean enableIfNecessary)
4440   {
4441     // note - currently this is only still here rather than in the controller
4442     // because of the featureSettings hard reference that is yet to be
4443     // abstracted
4444     if (enableIfNecessary)
4445     {
4446       viewport.setShowSequenceFeatures(true);
4447       showSeqFeatures.setSelected(true);
4448     }
4449
4450   }
4451
4452   @Override
4453   public void dragEnter(DropTargetDragEvent evt)
4454   {
4455   }
4456
4457   @Override
4458   public void dragExit(DropTargetEvent evt)
4459   {
4460   }
4461
4462   @Override
4463   public void dragOver(DropTargetDragEvent evt)
4464   {
4465   }
4466
4467   @Override
4468   public void dropActionChanged(DropTargetDragEvent evt)
4469   {
4470   }
4471
4472   @Override
4473   public void drop(DropTargetDropEvent evt)
4474   {
4475     // JAL-1552 - acceptDrop required before getTransferable call for
4476     // Java's Transferable for native dnd
4477     evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4478     Transferable t = evt.getTransferable();
4479
4480     final AlignFrame thisaf = this;
4481     final List<Object> files = new ArrayList<>();
4482     List<DataSourceType> protocols = new ArrayList<>();
4483
4484     try
4485     {
4486       Desktop.transferFromDropTarget(files, protocols, evt, t);
4487     } catch (Exception e)
4488     {
4489       e.printStackTrace();
4490     }
4491     if (files != null)
4492     {
4493       new Thread(new Runnable()
4494       {
4495         @Override
4496         public void run()
4497         {
4498           try
4499           {
4500             // check to see if any of these files have names matching sequences
4501             // in
4502             // the alignment
4503             SequenceIdMatcher idm = new SequenceIdMatcher(
4504                     viewport.getAlignment().getSequencesArray());
4505             /**
4506              * Object[] { String,SequenceI}
4507              */
4508             ArrayList<Object[]> filesmatched = new ArrayList<>();
4509             ArrayList<Object> filesnotmatched = new ArrayList<>();
4510             for (int i = 0; i < files.size(); i++)
4511             {
4512               // BH 2018
4513               Object file = files.get(i);
4514               String fileName = file.toString();
4515               String pdbfn = "";
4516               DataSourceType protocol = (file instanceof File
4517                       ? DataSourceType.FILE
4518                       : FormatAdapter.checkProtocol(fileName));
4519               if (protocol == DataSourceType.FILE)
4520               {
4521                 File fl = (file instanceof File ? (File) file
4522                         : new File(fileName));
4523                 pdbfn = fl.getName();
4524               }
4525               else if (protocol == DataSourceType.URL)
4526               {
4527                 URL url = new URL(fileName);
4528                 pdbfn = url.getFile();
4529               }
4530               if (pdbfn.length() > 0)
4531               {
4532                 // attempt to find a match in the alignment
4533                 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4534                 int l = 0, c = pdbfn.indexOf(".");
4535                 while (mtch == null && c != -1)
4536                 {
4537                   do
4538                   {
4539                     l = c;
4540                   } while ((c = pdbfn.indexOf(".", l)) > l);
4541                   if (l > -1)
4542                   {
4543                     pdbfn = pdbfn.substring(0, l);
4544                   }
4545                   mtch = idm.findAllIdMatches(pdbfn);
4546                 }
4547                 if (mtch != null)
4548                 {
4549                   FileFormatI type;
4550                   try
4551                   {
4552                     type = new IdentifyFile().identify(file, protocol);
4553                   } catch (Exception ex)
4554                   {
4555                     type = null;
4556                   }
4557                   if (type != null && type.isStructureFile())
4558                   {
4559                     filesmatched.add(new Object[] { file, protocol, mtch });
4560                     continue;
4561                   }
4562                 }
4563                 // File wasn't named like one of the sequences or wasn't a PDB
4564                 // file.
4565                 filesnotmatched.add(file);
4566               }
4567             }
4568             int assocfiles = 0;
4569             if (filesmatched.size() > 0)
4570             {
4571               boolean autoAssociate = Cache
4572                       .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4573               if (!autoAssociate)
4574               {
4575                 String msg = MessageManager.formatMessage(
4576                         "label.automatically_associate_structure_files_with_sequences_same_name",
4577                         new Object[]
4578                         { Integer.valueOf(filesmatched.size())
4579                                 .toString() });
4580                 String ttl = MessageManager.getString(
4581                         "label.automatically_associate_structure_files_by_name");
4582                 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4583                         ttl, JvOptionPane.YES_NO_OPTION);
4584                 autoAssociate = choice == JvOptionPane.YES_OPTION;
4585               }
4586               if (autoAssociate)
4587               {
4588                 for (Object[] fm : filesmatched)
4589                 {
4590                   // try and associate
4591                   // TODO: may want to set a standard ID naming formalism for
4592                   // associating PDB files which have no IDs.
4593                   for (SequenceI toassoc : (SequenceI[]) fm[2])
4594                   {
4595                     PDBEntry pe = new AssociatePdbFileWithSeq()
4596                             .associatePdbWithSeq(fm[0].toString(),
4597                                     (DataSourceType) fm[1], toassoc, false,
4598                                     Desktop.instance);
4599                     if (pe != null)
4600                     {
4601                       System.err.println("Associated file : "
4602                               + (fm[0].toString()) + " with "
4603                               + toassoc.getDisplayId(true));
4604                       assocfiles++;
4605                     }
4606                   }
4607                   // TODO: do we need to update overview ? only if features are
4608                   // shown I guess
4609                   alignPanel.paintAlignment(true, false);
4610                 }
4611               }
4612               else
4613               {
4614                 /*
4615                  * add declined structures as sequences
4616                  */
4617                 for (Object[] o : filesmatched)
4618                 {
4619                   filesnotmatched.add(o[0]);
4620                 }
4621               }
4622             }
4623             if (filesnotmatched.size() > 0)
4624             {
4625               if (assocfiles > 0 && (Cache.getDefault(
4626                       "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4627                       || JvOptionPane.showConfirmDialog(thisaf,
4628                               "<html>" + MessageManager.formatMessage(
4629                                       "label.ignore_unmatched_dropped_files_info",
4630                                       new Object[]
4631                                       { Integer.valueOf(
4632                                               filesnotmatched.size())
4633                                               .toString() })
4634                                       + "</html>",
4635                               MessageManager.getString(
4636                                       "label.ignore_unmatched_dropped_files"),
4637                               JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4638               {
4639                 return;
4640               }
4641               for (Object fn : filesnotmatched)
4642               {
4643                 loadJalviewDataFile(fn, null, null, null);
4644               }
4645
4646             }
4647           } catch (Exception ex)
4648           {
4649             ex.printStackTrace();
4650           }
4651         }
4652       }).start();
4653     }
4654   }
4655
4656   /**
4657    * Attempt to load a "dropped" file or URL string, by testing in turn for
4658    * <ul>
4659    * <li>an Annotation file</li>
4660    * <li>a JNet file</li>
4661    * <li>a features file</li>
4662    * <li>else try to interpret as an alignment file</li>
4663    * </ul>
4664    *
4665    * @param file
4666    *          either a filename or a URL string.
4667    */
4668   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4669           FileFormatI format, SequenceI assocSeq)
4670   {
4671     // BH 2018 was String file
4672     try
4673     {
4674       if (sourceType == null)
4675       {
4676         sourceType = FormatAdapter.checkProtocol(file);
4677       }
4678       // if the file isn't identified, or not positively identified as some
4679       // other filetype (PFAM is default unidentified alignment file type) then
4680       // try to parse as annotation.
4681       boolean isAnnotation = (format == null
4682               || FileFormat.Pfam.equals(format))
4683                       ? new AnnotationFile().annotateAlignmentView(viewport,
4684                               file, sourceType)
4685                       : false;
4686
4687       if (!isAnnotation)
4688       {
4689         // first see if its a T-COFFEE score file
4690         TCoffeeScoreFile tcf = null;
4691         try
4692         {
4693           tcf = new TCoffeeScoreFile(file, sourceType);
4694           if (tcf.isValid())
4695           {
4696             if (tcf.annotateAlignment(viewport.getAlignment(), true))
4697             {
4698               buildColourMenu();
4699               changeColour(
4700                       new TCoffeeColourScheme(viewport.getAlignment()));
4701               isAnnotation = true;
4702               setStatus(MessageManager.getString(
4703                       "label.successfully_pasted_tcoffee_scores_to_alignment"));
4704             }
4705             else
4706             {
4707               // some problem - if no warning its probable that the ID matching
4708               // process didn't work
4709               JvOptionPane.showMessageDialog(Desktop.desktop,
4710                       tcf.getWarningMessage() == null
4711                               ? MessageManager.getString(
4712                                       "label.check_file_matches_sequence_ids_alignment")
4713                               : tcf.getWarningMessage(),
4714                       MessageManager.getString(
4715                               "label.problem_reading_tcoffee_score_file"),
4716                       JvOptionPane.WARNING_MESSAGE);
4717             }
4718           }
4719           else
4720           {
4721             tcf = null;
4722           }
4723         } catch (Exception x)
4724         {
4725           Cache.log.debug(
4726                   "Exception when processing data source as T-COFFEE score file",
4727                   x);
4728           tcf = null;
4729         }
4730         if (tcf == null)
4731         {
4732           // try to see if its a JNet 'concise' style annotation file *before*
4733           // we
4734           // try to parse it as a features file
4735           if (format == null)
4736           {
4737             format = new IdentifyFile().identify(file, sourceType);
4738           }
4739           if (FileFormat.ScoreMatrix == format)
4740           {
4741             ScoreMatrixFile sm = new ScoreMatrixFile(
4742                     new FileParse(file, sourceType));
4743             sm.parse();
4744             // todo: i18n this message
4745             setStatus(MessageManager.formatMessage(
4746                     "label.successfully_loaded_matrix",
4747                     sm.getMatrixName()));
4748           }
4749           else if (FileFormat.Jnet.equals(format))
4750           {
4751             JPredFile predictions = new JPredFile(file, sourceType);
4752             new JnetAnnotationMaker();
4753             JnetAnnotationMaker.add_annotation(predictions,
4754                     viewport.getAlignment(), 0, false);
4755             viewport.getAlignment().setupJPredAlignment();
4756             isAnnotation = true;
4757           }
4758           // else if (IdentifyFile.FeaturesFile.equals(format))
4759           else if (FileFormat.Features.equals(format))
4760           {
4761             if (parseFeaturesFile(file, sourceType))
4762             {
4763               alignPanel.paintAlignment(true, true);
4764             }
4765           }
4766           else
4767           {
4768             new FileLoader().LoadFile(viewport, file, sourceType, format);
4769           }
4770         }
4771       }
4772       if (isAnnotation)
4773       {
4774
4775         alignPanel.adjustAnnotationHeight();
4776         viewport.updateSequenceIdColours();
4777         buildSortByAnnotationScoresMenu();
4778         alignPanel.paintAlignment(true, true);
4779       }
4780     } catch (Exception ex)
4781     {
4782       ex.printStackTrace();
4783     } catch (OutOfMemoryError oom)
4784     {
4785       try
4786       {
4787         System.gc();
4788       } catch (Exception x)
4789       {
4790       }
4791       new OOMWarning(
4792               "loading data "
4793                       + (sourceType != null
4794                               ? (sourceType == DataSourceType.PASTE
4795                                       ? "from clipboard."
4796                                       : "using " + sourceType + " from "
4797                                               + file)
4798                               : ".")
4799                       + (format != null
4800                               ? "(parsing as '" + format + "' file)"
4801                               : ""),
4802               oom, Desktop.desktop);
4803     }
4804   }
4805
4806   /**
4807    * Method invoked by the ChangeListener on the tabbed pane, in other words
4808    * when a different tabbed pane is selected by the user or programmatically.
4809    */
4810   @Override
4811   public void tabSelectionChanged(int index)
4812   {
4813     if (index > -1)
4814     {
4815       alignPanel = alignPanels.get(index);
4816       viewport = alignPanel.av;
4817       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4818       setMenusFromViewport(viewport);
4819     }
4820
4821     /*
4822      * 'focus' any colour slider that is open to the selected viewport
4823      */
4824     if (viewport.getConservationSelected())
4825     {
4826       SliderPanel.setConservationSlider(alignPanel,
4827               viewport.getResidueShading(), alignPanel.getViewName());
4828     }
4829     else
4830     {
4831       SliderPanel.hideConservationSlider();
4832     }
4833     if (viewport.getAbovePIDThreshold())
4834     {
4835       SliderPanel.setPIDSliderSource(alignPanel,
4836               viewport.getResidueShading(), alignPanel.getViewName());
4837     }
4838     else
4839     {
4840       SliderPanel.hidePIDSlider();
4841     }
4842
4843     /*
4844      * If there is a frame linked to this one in a SplitPane, switch it to the
4845      * same view tab index. No infinite recursion of calls should happen, since
4846      * tabSelectionChanged() should not get invoked on setting the selected
4847      * index to an unchanged value. Guard against setting an invalid index
4848      * before the new view peer tab has been created.
4849      */
4850     final AlignViewportI peer = viewport.getCodingComplement();
4851     if (peer != null)
4852     {
4853       AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4854               .getAlignPanel().alignFrame;
4855       if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4856       {
4857         linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4858       }
4859     }
4860   }
4861
4862   /**
4863    * On right mouse click on view tab, prompt for and set new view name.
4864    */
4865   @Override
4866   public void tabbedPane_mousePressed(MouseEvent e)
4867   {
4868     if (e.isPopupTrigger())
4869     {
4870       String msg = MessageManager.getString("label.enter_view_name");
4871       String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
4872       String reply = JvOptionPane.showInputDialog(msg, ttl);
4873
4874       if (reply != null)
4875       {
4876         viewport.setViewName(reply);
4877         // TODO warn if reply is in getExistingViewNames()?
4878         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4879       }
4880     }
4881   }
4882
4883   public AlignViewport getCurrentView()
4884   {
4885     return viewport;
4886   }
4887
4888   /**
4889    * Open the dialog for regex description parsing.
4890    */
4891   @Override
4892   protected void extractScores_actionPerformed(ActionEvent e)
4893   {
4894     ParseProperties pp = new jalview.analysis.ParseProperties(
4895             viewport.getAlignment());
4896     // TODO: verify regex and introduce GUI dialog for version 2.5
4897     // if (pp.getScoresFromDescription("col", "score column ",
4898     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4899     // true)>0)
4900     if (pp.getScoresFromDescription("description column",
4901             "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4902     {
4903       buildSortByAnnotationScoresMenu();
4904     }
4905   }
4906
4907   /*
4908    * (non-Javadoc)
4909    *
4910    * @see
4911    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4912    * )
4913    */
4914   @Override
4915   protected void showDbRefs_actionPerformed(ActionEvent e)
4916   {
4917     viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4918   }
4919
4920   /*
4921    * (non-Javadoc)
4922    *
4923    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4924    * ActionEvent)
4925    */
4926   @Override
4927   protected void showNpFeats_actionPerformed(ActionEvent e)
4928   {
4929     viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4930   }
4931
4932   /**
4933    * find the viewport amongst the tabs in this alignment frame and close that
4934    * tab
4935    *
4936    * @param av
4937    */
4938   public boolean closeView(AlignViewportI av)
4939   {
4940     if (viewport == av)
4941     {
4942       this.closeMenuItem_actionPerformed(false);
4943       return true;
4944     }
4945     Component[] comp = tabbedPane.getComponents();
4946     for (int i = 0; comp != null && i < comp.length; i++)
4947     {
4948       if (comp[i] instanceof AlignmentPanel)
4949       {
4950         if (((AlignmentPanel) comp[i]).av == av)
4951         {
4952           // close the view.
4953           closeView((AlignmentPanel) comp[i]);
4954           return true;
4955         }
4956       }
4957     }
4958     return false;
4959   }
4960
4961   protected void build_fetchdbmenu(JMenu webService)
4962   {
4963     // Temporary hack - DBRef Fetcher always top level ws entry.
4964     // TODO We probably want to store a sequence database checklist in
4965     // preferences and have checkboxes.. rather than individual sources selected
4966     // here
4967     final JMenu rfetch = new JMenu(
4968             MessageManager.getString("action.fetch_db_references"));
4969     rfetch.setToolTipText(MessageManager.getString(
4970             "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
4971     webService.add(rfetch);
4972
4973     final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
4974             MessageManager.getString("option.trim_retrieved_seqs"));
4975     trimrs.setToolTipText(
4976             MessageManager.getString("label.trim_retrieved_sequences"));
4977     trimrs.setSelected(
4978             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
4979     trimrs.addActionListener(new ActionListener()
4980     {
4981       @Override
4982       public void actionPerformed(ActionEvent e)
4983       {
4984         trimrs.setSelected(trimrs.isSelected());
4985         Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
4986                 Boolean.valueOf(trimrs.isSelected()).toString());
4987       };
4988     });
4989     rfetch.add(trimrs);
4990     JMenuItem fetchr = new JMenuItem(
4991             MessageManager.getString("label.standard_databases"));
4992     fetchr.setToolTipText(
4993             MessageManager.getString("label.fetch_embl_uniprot"));
4994     fetchr.addActionListener(new ActionListener()
4995     {
4996
4997       @Override
4998       public void actionPerformed(ActionEvent e)
4999       {
5000         new Thread(new Runnable()
5001         {
5002           @Override
5003           public void run()
5004           {
5005             boolean isNucleotide = alignPanel.alignFrame.getViewport()
5006                     .getAlignment().isNucleotide();
5007             DBRefFetcher dbRefFetcher = new DBRefFetcher(
5008                     alignPanel.av.getSequenceSelection(),
5009                     alignPanel.alignFrame, null,
5010                     alignPanel.alignFrame.featureSettings, isNucleotide);
5011             dbRefFetcher.addListener(new FetchFinishedListenerI()
5012             {
5013               @Override
5014               public void finished()
5015               {
5016                 AlignFrame.this.setMenusForViewport();
5017               }
5018             });
5019             dbRefFetcher.fetchDBRefs(false);
5020           }
5021         }).start();
5022
5023       }
5024
5025     });
5026     rfetch.add(fetchr);
5027     new Thread(new Runnable()
5028     {
5029       @Override
5030       public void run()
5031       {
5032         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5033                 .getSequenceFetcherSingleton();
5034         javax.swing.SwingUtilities.invokeLater(new Runnable()
5035         {
5036           @Override
5037           public void run()
5038           {
5039             String[] dbclasses = sf.getNonAlignmentSources();
5040             List<DbSourceProxy> otherdb;
5041             JMenu dfetch = new JMenu();
5042             JMenu ifetch = new JMenu();
5043             JMenuItem fetchr = null;
5044             int comp = 0, icomp = 0, mcomp = 15;
5045             String mname = null;
5046             int dbi = 0;
5047             for (String dbclass : dbclasses)
5048             {
5049               otherdb = sf.getSourceProxy(dbclass);
5050               // add a single entry for this class, or submenu allowing 'fetch
5051               // all' or pick one
5052               if (otherdb == null || otherdb.size() < 1)
5053               {
5054                 continue;
5055               }
5056               if (mname == null)
5057               {
5058                 mname = "From " + dbclass;
5059               }
5060               if (otherdb.size() == 1)
5061               {
5062                 final DbSourceProxy[] dassource = otherdb
5063                         .toArray(new DbSourceProxy[0]);
5064                 DbSourceProxy src = otherdb.get(0);
5065                 fetchr = new JMenuItem(src.getDbSource());
5066                 fetchr.addActionListener(new ActionListener()
5067                 {
5068
5069                   @Override
5070                   public void actionPerformed(ActionEvent e)
5071                   {
5072                     new Thread(new Runnable()
5073                     {
5074
5075                       @Override
5076                       public void run()
5077                       {
5078                         boolean isNucleotide = alignPanel.alignFrame
5079                                 .getViewport().getAlignment()
5080                                 .isNucleotide();
5081                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5082                                 alignPanel.av.getSequenceSelection(),
5083                                 alignPanel.alignFrame, dassource,
5084                                 alignPanel.alignFrame.featureSettings,
5085                                 isNucleotide);
5086                         dbRefFetcher
5087                                 .addListener(new FetchFinishedListenerI()
5088                                 {
5089                                   @Override
5090                                   public void finished()
5091                                   {
5092                                     AlignFrame.this.setMenusForViewport();
5093                                   }
5094                                 });
5095                         dbRefFetcher.fetchDBRefs(false);
5096                       }
5097                     }).start();
5098                   }
5099
5100                 });
5101                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5102                         MessageManager.formatMessage(
5103                                 "label.fetch_retrieve_from", new Object[]
5104                                 { src.getDbName() })));
5105                 dfetch.add(fetchr);
5106                 comp++;
5107               }
5108               else
5109               {
5110                 final DbSourceProxy[] dassource = otherdb
5111                         .toArray(new DbSourceProxy[0]);
5112                 // fetch all entry
5113                 DbSourceProxy src = otherdb.get(0);
5114                 fetchr = new JMenuItem(MessageManager
5115                         .formatMessage("label.fetch_all_param", new Object[]
5116                         { src.getDbSource() }));
5117                 fetchr.addActionListener(new ActionListener()
5118                 {
5119                   @Override
5120                   public void actionPerformed(ActionEvent e)
5121                   {
5122                     new Thread(new Runnable()
5123                     {
5124
5125                       @Override
5126                       public void run()
5127                       {
5128                         boolean isNucleotide = alignPanel.alignFrame
5129                                 .getViewport().getAlignment()
5130                                 .isNucleotide();
5131                         DBRefFetcher dbRefFetcher = new DBRefFetcher(
5132                                 alignPanel.av.getSequenceSelection(),
5133                                 alignPanel.alignFrame, dassource,
5134                                 alignPanel.alignFrame.featureSettings,
5135                                 isNucleotide);
5136                         dbRefFetcher
5137                                 .addListener(new FetchFinishedListenerI()
5138                                 {
5139                                   @Override
5140                                   public void finished()
5141                                   {
5142                                     AlignFrame.this.setMenusForViewport();
5143                                   }
5144                                 });
5145                         dbRefFetcher.fetchDBRefs(false);
5146                       }
5147                     }).start();
5148                   }
5149                 });
5150
5151                 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5152                         MessageManager.formatMessage(
5153                                 "label.fetch_retrieve_from_all_sources",
5154                                 new Object[]
5155                                 { Integer.valueOf(otherdb.size())
5156                                         .toString(),
5157                                     src.getDbSource(), src.getDbName() })));
5158                 dfetch.add(fetchr);
5159                 comp++;
5160                 // and then build the rest of the individual menus
5161                 ifetch = new JMenu(MessageManager.formatMessage(
5162                         "label.source_from_db_source", new Object[]
5163                         { src.getDbSource() }));
5164                 icomp = 0;
5165                 String imname = null;
5166                 int i = 0;
5167                 for (DbSourceProxy sproxy : otherdb)
5168                 {
5169                   String dbname = sproxy.getDbName();
5170                   String sname = dbname.length() > 5
5171                           ? dbname.substring(0, 5) + "..."
5172                           : dbname;
5173                   String msname = dbname.length() > 10
5174                           ? dbname.substring(0, 10) + "..."
5175                           : dbname;
5176                   if (imname == null)
5177                   {
5178                     imname = MessageManager
5179                             .formatMessage("label.from_msname", new Object[]
5180                             { sname });
5181                   }
5182                   fetchr = new JMenuItem(msname);
5183                   final DbSourceProxy[] dassrc = { sproxy };
5184                   fetchr.addActionListener(new ActionListener()
5185                   {
5186
5187                     @Override
5188                     public void actionPerformed(ActionEvent e)
5189                     {
5190                       new Thread(new Runnable()
5191                       {
5192
5193                         @Override
5194                         public void run()
5195                         {
5196                           boolean isNucleotide = alignPanel.alignFrame
5197                                   .getViewport().getAlignment()
5198                                   .isNucleotide();
5199                           DBRefFetcher dbRefFetcher = new DBRefFetcher(
5200                                   alignPanel.av.getSequenceSelection(),
5201                                   alignPanel.alignFrame, dassrc,
5202                                   alignPanel.alignFrame.featureSettings,
5203                                   isNucleotide);
5204                           dbRefFetcher
5205                                   .addListener(new FetchFinishedListenerI()
5206                                   {
5207                                     @Override
5208                                     public void finished()
5209                                     {
5210                                       AlignFrame.this.setMenusForViewport();
5211                                     }
5212                                   });
5213                           dbRefFetcher.fetchDBRefs(false);
5214                         }
5215                       }).start();
5216                     }
5217
5218                   });
5219                   fetchr.setToolTipText(
5220                           "<html>" + MessageManager.formatMessage(
5221                                   "label.fetch_retrieve_from", new Object[]
5222                                   { dbname }));
5223                   ifetch.add(fetchr);
5224                   ++i;
5225                   if (++icomp >= mcomp || i == (otherdb.size()))
5226                   {
5227                     ifetch.setText(MessageManager.formatMessage(
5228                             "label.source_to_target", imname, sname));
5229                     dfetch.add(ifetch);
5230                     ifetch = new JMenu();
5231                     imname = null;
5232                     icomp = 0;
5233                     comp++;
5234                   }
5235                 }
5236               }
5237               ++dbi;
5238               if (comp >= mcomp || dbi >= (dbclasses.length))
5239               {
5240                 dfetch.setText(MessageManager.formatMessage(
5241                         "label.source_to_target", mname, dbclass));
5242                 rfetch.add(dfetch);
5243                 dfetch = new JMenu();
5244                 mname = null;
5245                 comp = 0;
5246               }
5247             }
5248           }
5249         });
5250       }
5251     }).start();
5252
5253   }
5254
5255   /**
5256    * Left justify the whole alignment.
5257    */
5258   @Override
5259   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5260   {
5261     AlignmentI al = viewport.getAlignment();
5262     al.justify(false);
5263     viewport.firePropertyChange("alignment", null, al);
5264   }
5265
5266   /**
5267    * Right justify the whole alignment.
5268    */
5269   @Override
5270   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5271   {
5272     AlignmentI al = viewport.getAlignment();
5273     al.justify(true);
5274     viewport.firePropertyChange("alignment", null, al);
5275   }
5276
5277   @Override
5278   public void setShowSeqFeatures(boolean b)
5279   {
5280     showSeqFeatures.setSelected(b);
5281     viewport.setShowSequenceFeatures(b);
5282   }
5283
5284   /*
5285    * (non-Javadoc)
5286    *
5287    * @see
5288    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5289    * awt.event.ActionEvent)
5290    */
5291   @Override
5292   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5293   {
5294     viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5295     alignPanel.paintAlignment(false, false);
5296   }
5297
5298   /*
5299    * (non-Javadoc)
5300    *
5301    * @see
5302    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5303    * .ActionEvent)
5304    */
5305   @Override
5306   protected void showGroupConsensus_actionPerformed(ActionEvent e)
5307   {
5308     viewport.setShowGroupConsensus(showGroupConsensus.getState());
5309     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5310
5311   }
5312
5313   /*
5314    * (non-Javadoc)
5315    *
5316    * @see
5317    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5318    * .event.ActionEvent)
5319    */
5320   @Override
5321   protected void showGroupConservation_actionPerformed(ActionEvent e)
5322   {
5323     viewport.setShowGroupConservation(showGroupConservation.getState());
5324     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5325   }
5326
5327   /*
5328    * (non-Javadoc)
5329    *
5330    * @see
5331    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5332    * .event.ActionEvent)
5333    */
5334   @Override
5335   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5336   {
5337     viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5338     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5339   }
5340
5341   /*
5342    * (non-Javadoc)
5343    *
5344    * @see
5345    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5346    * .event.ActionEvent)
5347    */
5348   @Override
5349   protected void showSequenceLogo_actionPerformed(ActionEvent e)
5350   {
5351     viewport.setShowSequenceLogo(showSequenceLogo.getState());
5352     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5353   }
5354
5355   @Override
5356   protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5357   {
5358     showSequenceLogo.setState(true);
5359     viewport.setShowSequenceLogo(true);
5360     viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5361     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5362   }
5363
5364   @Override
5365   protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5366   {
5367     alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5368   }
5369
5370   /*
5371    * (non-Javadoc)
5372    *
5373    * @see
5374    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5375    * .event.ActionEvent)
5376    */
5377   @Override
5378   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5379   {
5380     if (avc.makeGroupsFromSelection())
5381     {
5382       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5383       alignPanel.updateAnnotation();
5384       alignPanel.paintAlignment(true, true);
5385     }
5386   }
5387
5388   public void clearAlignmentSeqRep()
5389   {
5390     // TODO refactor alignmentseqrep to controller
5391     if (viewport.getAlignment().hasSeqrep())
5392     {
5393       viewport.getAlignment().setSeqrep(null);
5394       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5395       alignPanel.updateAnnotation();
5396       alignPanel.paintAlignment(true, true);
5397     }
5398   }
5399
5400   @Override
5401   protected void createGroup_actionPerformed(ActionEvent e)
5402   {
5403     if (avc.createGroup())
5404     {
5405       if (applyAutoAnnotationSettings.isSelected())
5406       {
5407         alignPanel.updateAnnotation(true, false);
5408       }
5409       alignPanel.alignmentChanged();
5410     }
5411   }
5412
5413   @Override
5414   protected void unGroup_actionPerformed(ActionEvent e)
5415   {
5416     if (avc.unGroup())
5417     {
5418       alignPanel.alignmentChanged();
5419     }
5420   }
5421
5422   /**
5423    * make the given alignmentPanel the currently selected tab
5424    *
5425    * @param alignmentPanel
5426    */
5427   public void setDisplayedView(AlignmentPanel alignmentPanel)
5428   {
5429     if (!viewport.getSequenceSetId()
5430             .equals(alignmentPanel.av.getSequenceSetId()))
5431     {
5432       throw new Error(MessageManager.getString(
5433               "error.implementation_error_cannot_show_view_alignment_frame"));
5434     }
5435     if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5436             .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5437     {
5438       tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5439     }
5440   }
5441
5442   /**
5443    * Action on selection of menu options to Show or Hide annotations.
5444    *
5445    * @param visible
5446    * @param forSequences
5447    *          update sequence-related annotations
5448    * @param forAlignment
5449    *          update non-sequence-related annotations
5450    */
5451   @Override
5452   protected void setAnnotationsVisibility(boolean visible,
5453           boolean forSequences, boolean forAlignment)
5454   {
5455     AlignmentAnnotation[] anns = alignPanel.getAlignment()
5456             .getAlignmentAnnotation();
5457     if (anns == null)
5458     {
5459       return;
5460     }
5461     for (AlignmentAnnotation aa : anns)
5462     {
5463       /*
5464        * don't display non-positional annotations on an alignment
5465        */
5466       if (aa.annotations == null)
5467       {
5468         continue;
5469       }
5470       boolean apply = (aa.sequenceRef == null && forAlignment)
5471               || (aa.sequenceRef != null && forSequences);
5472       if (apply)
5473       {
5474         aa.visible = visible;
5475       }
5476     }
5477     alignPanel.validateAnnotationDimensions(true);
5478     alignPanel.alignmentChanged();
5479   }
5480
5481   /**
5482    * Store selected annotation sort order for the view and repaint.
5483    */
5484   @Override
5485   protected void sortAnnotations_actionPerformed()
5486   {
5487     this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5488     this.alignPanel.av
5489             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5490     alignPanel.paintAlignment(false, false);
5491   }
5492
5493   /**
5494    *
5495    * @return alignment panels in this alignment frame
5496    */
5497   public List<? extends AlignmentViewPanel> getAlignPanels()
5498   {
5499     // alignPanels is never null
5500     // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5501     return alignPanels;
5502   }
5503
5504   /**
5505    * Open a new alignment window, with the cDNA associated with this (protein)
5506    * alignment, aligned as is the protein.
5507    */
5508   protected void viewAsCdna_actionPerformed()
5509   {
5510     // TODO no longer a menu action - refactor as required
5511     final AlignmentI alignment = getViewport().getAlignment();
5512     List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5513     if (mappings == null)
5514     {
5515       return;
5516     }
5517     List<SequenceI> cdnaSeqs = new ArrayList<>();
5518     for (SequenceI aaSeq : alignment.getSequences())
5519     {
5520       for (AlignedCodonFrame acf : mappings)
5521       {
5522         SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5523         if (dnaSeq != null)
5524         {
5525           /*
5526            * There is a cDNA mapping for this protein sequence - add to new
5527            * alignment. It will share the same dataset sequence as other mapped
5528            * cDNA (no new mappings need to be created).
5529            */
5530           final Sequence newSeq = new Sequence(dnaSeq);
5531           newSeq.setDatasetSequence(dnaSeq);
5532           cdnaSeqs.add(newSeq);
5533         }
5534       }
5535     }
5536     if (cdnaSeqs.size() == 0)
5537     {
5538       // show a warning dialog no mapped cDNA
5539       return;
5540     }
5541     AlignmentI cdna = new Alignment(
5542             cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5543     GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5544             AlignFrame.DEFAULT_HEIGHT);
5545     cdna.alignAs(alignment);
5546     String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5547             + this.title;
5548     Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5549             AlignFrame.DEFAULT_HEIGHT);
5550   }
5551
5552   /**
5553    * Set visibility of dna/protein complement view (available when shown in a
5554    * split frame).
5555    *
5556    * @param show
5557    */
5558   @Override
5559   protected void showComplement_actionPerformed(boolean show)
5560   {
5561     SplitContainerI sf = getSplitViewContainer();
5562     if (sf != null)
5563     {
5564       sf.setComplementVisible(this, show);
5565     }
5566   }
5567
5568   /**
5569    * Generate the reverse (optionally complemented) of the selected sequences,
5570    * and add them to the alignment
5571    */
5572   @Override
5573   protected void showReverse_actionPerformed(boolean complement)
5574   {
5575     AlignmentI al = null;
5576     try
5577     {
5578       Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5579       al = dna.reverseCdna(complement);
5580       viewport.addAlignment(al, "");
5581       addHistoryItem(new EditCommand(
5582               MessageManager.getString("label.add_sequences"), Action.PASTE,
5583               al.getSequencesArray(), 0, al.getWidth(),
5584               viewport.getAlignment()));
5585     } catch (Exception ex)
5586     {
5587       System.err.println(ex.getMessage());
5588       return;
5589     }
5590   }
5591
5592   /**
5593    * Try to run a script in the Groovy console, having first ensured that this
5594    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5595    * be targeted at this alignment.
5596    */
5597   @Override
5598   protected void runGroovy_actionPerformed()
5599   {
5600     Jalview.setCurrentAlignFrame(this);
5601     groovy.ui.Console console = Desktop.getGroovyConsole();
5602     if (console != null)
5603     {
5604       try
5605       {
5606         console.runScript();
5607       } catch (Exception ex)
5608       {
5609         System.err.println((ex.toString()));
5610         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5611                 MessageManager.getString("label.couldnt_run_groovy_script"),
5612                 MessageManager.getString("label.groovy_support_failed"),
5613                 JvOptionPane.ERROR_MESSAGE);
5614       }
5615     }
5616     else
5617     {
5618       System.err.println("Can't run Groovy script as console not found");
5619     }
5620   }
5621
5622   /**
5623    * Hides columns containing (or not containing) a specified feature, provided
5624    * that would not leave all columns hidden
5625    *
5626    * @param featureType
5627    * @param columnsContaining
5628    * @return
5629    */
5630   public boolean hideFeatureColumns(String featureType,
5631           boolean columnsContaining)
5632   {
5633     boolean notForHiding = avc.markColumnsContainingFeatures(
5634             columnsContaining, false, false, featureType);
5635     if (notForHiding)
5636     {
5637       if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5638               false, featureType))
5639       {
5640         getViewport().hideSelectedColumns();
5641         return true;
5642       }
5643     }
5644     return false;
5645   }
5646
5647   @Override
5648   protected void selectHighlightedColumns_actionPerformed(
5649           ActionEvent actionEvent)
5650   {
5651     // include key modifier check in case user selects from menu
5652     avc.markHighlightedColumns(
5653             (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5654             (actionEvent.getModifiers() & (ActionEvent.META_MASK
5655                     | ActionEvent.CTRL_MASK)) != 0);
5656   }
5657
5658   /**
5659    * Rebuilds the Colour menu, including any user-defined colours which have
5660    * been loaded either on startup or during the session
5661    */
5662   public void buildColourMenu()
5663   {
5664     colourMenu.removeAll();
5665
5666     colourMenu.add(applyToAllGroups);
5667     colourMenu.add(textColour);
5668     colourMenu.addSeparator();
5669
5670     ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
5671             false);
5672
5673     colourMenu.addSeparator();
5674     colourMenu.add(conservationMenuItem);
5675     colourMenu.add(modifyConservation);
5676     colourMenu.add(abovePIDThreshold);
5677     colourMenu.add(modifyPID);
5678     colourMenu.add(annotationColour);
5679
5680     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5681     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5682   }
5683
5684   /**
5685    * Open a dialog (if not already open) that allows the user to select and
5686    * calculate PCA or Tree analysis
5687    */
5688   protected void openTreePcaDialog()
5689   {
5690     if (alignPanel.getCalculationDialog() == null)
5691     {
5692       new CalculationChooser(AlignFrame.this);
5693     }
5694   }
5695
5696   @Override
5697   protected void loadVcf_actionPerformed()
5698   {
5699     JalviewFileChooser chooser = new JalviewFileChooser(
5700             Cache.getProperty("LAST_DIRECTORY"));
5701     chooser.setFileView(new JalviewFileView());
5702     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5703     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5704     final AlignFrame us = this;
5705     chooser.setResponseHandler(0, new Runnable()
5706     {
5707       @Override
5708       public void run()
5709       {
5710         String choice = chooser.getSelectedFile().getPath();
5711         Cache.setProperty("LAST_DIRECTORY", choice);
5712         SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5713         new VCFLoader(choice).loadVCF(seqs, us);
5714       };
5715     });
5716     chooser.showOpenDialog(null);
5717
5718   }
5719
5720 }
5721
5722 class PrintThread extends Thread
5723 {
5724   AlignmentPanel ap;
5725
5726   public PrintThread(AlignmentPanel ap)
5727   {
5728     this.ap = ap;
5729   }
5730
5731   static PageFormat pf;
5732
5733   @Override
5734   public void run()
5735   {
5736     PrinterJob printJob = PrinterJob.getPrinterJob();
5737
5738     if (pf != null)
5739     {
5740       printJob.setPrintable(ap, pf);
5741     }
5742     else
5743     {
5744       printJob.setPrintable(ap);
5745     }
5746
5747     if (printJob.printDialog())
5748     {
5749       try
5750       {
5751         printJob.print();
5752       } catch (Exception PrintException)
5753       {
5754         PrintException.printStackTrace();
5755       }
5756     }
5757   }
5758 }