src/jalview/gui/AlignFrame.java

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